Murray and Callum Davidson combined to help secure a St Johnstone win that means double trouble for Dunfermline's hopes of avoiding relegation.
A Liam Craig free-kick crashed against a Pars post before Murray swept home his side's 33rd-minute opener.
Callum broke clear to finish clinically two minutes later.
Paul Burns fired a reply in a rare attack after 73 minutes, but Lee Croft killed off the game with a fine third five minutes later.
And their first defeat in 18 years at at McDiarmid Park leaves the Pars three points adrift of Hibernian at the foot of the table after the Leith side's 3-1 win away to Kilmarnock.
Croft came into the Saints midfield in place of Chris Millar following the goalless draw with Aberdeen.
Austin McCann, Gary Mason and Martin Hardie were restored to the Pars' starting line-up in place of Paul Burns, Kyle Hutton and Kevin Rutkiewicz after their midweek defeat by Celtic.
Different personnel, the same result, with the Pars on the back foot from the start and again being pinned back in their own half, with the home side dominating possession.
Francisco Sandaza was looking lively and several dangerous crosses were fired in, but Dunfermline held firm.
St Johnstone were dealt a blow in 15 minutes when Jody Morris limped off, being replaced with Millar.
Dunfermline goalkeeper Chris Smith, who had been excellent at Celtic Park, pulled off a superb double save.
First, he dived to his right to keep out Lee Croft's drive and then somehow clawed Sandaza's rebound effort off the line.
St Johnstone kept pressing and Frazer Wright's goalbound header was blocked by Paddy Boyle.
Saints were inches away from taking the lead after 26 minutes, when Liam Craig's inswinging free-kick missed everyone and smashed off the post before being scrambled clear.
Sandaza's movement was exceptional and a lovely flick released Croft, but his low shot was gathered by Smith.
Murray Davidson was next to try his luck with a turn and low drive after 32 minutes, but Smith saved well again only to be beaten a minute later.
Croft's chip was headed into the box by Millar and Murray Davidson swept home after good work from Sandaza.
In St Johnstone's next attack, it was 2-0. Sandaza found space in the box and fed Callum Davidson with a sublime reverse pass.
The full-back raced clear on goal and made no mistake with his finish from eight yards.
Dunfermline manager Jim McIntyre had already replaced David Graham with Paul Burns before half-time and brought on Paul Willis for Pat Boyle during the break, then Andy Kirk was soon replacing Liam Buchanan as he looked to rescue something from the game.
Still St Johnstone dominated and Sandaza twisted and turned before shooting narrowly wide.
Lee Croft smashed a rising drive off the upright in 69 minutes as St Johnstone chased a third.
However, it was Dunfermline who grabbed an unexpected lifeline, when Burns' curling shot came through a sea of bodies and nestled in the corner.
St Johnstone regrouped and Craig sent one drive wide and had another saved by Smith.
But Saints would not be denied for long and Croft made it 3-1 with a precise finish from 12 yards after some great skill.
Cillian Sheridan then hit the post in injury time as the hosts ended a run of three successive home defeats and left the Pars with only one win since 5 November.
St Johnstone manager Steve Lomas : "If you look at budgets, we probably shouldn't be battling for top six. But we are and the players are a victim of their own success as there's an expectation now.
"But we aren't getting too far ahead at the moment. There are many more tests to come and we can't get ahead of ourselves. Football can change in the space of 10 seconds.
"It was an important win. We got a great point at Aberdeen last week and it was vital to build on that.
"It was a fantastic performance and the scoreline could have been even bigger than it was."
Dunfermline Athletic manager Jim McIntyre : "The overall scoreline flattered us. We were lucky to only be 2-0 down at the break.
"We have been praised for our fighting spirit in the last few months, but I didn't see any of that.
"We just weren't good enough. There are no excuses. It was our worst performance in months.
"We got what we deserved and, although it's been a heavy week, we are miles better than what we showed.
"Maybe the Celtic game in midweek took more out of them than I thought, but that's still not an excuse."
- 15 Mannus
- 02 MacKay
- 03 Davidson
- 05 Wright
- 18 McCracken
- 04 Morris (Millar - 13' )
- 08 Davidson
- 09 Croft (Keatings - 87' )
- 10 Craig
- 11 Sheridan
- 21 Sandaza (Haber - 76' )
- 01 Enckelman
- 12 Maybury
- 07 Millar
- 34 Keiran Stewart
- 22 Oyenuga
- 23 Haber
- 46 Keatings
- 20 Smith
- 03 McCann
- 06 Keddie
- 13 Boyle (Willis - 46' )
- 15 Dowie
- 04 Mason
- 07 Cardle
- 08 Hardie
- 23 Thomson
- 11 Graham (Burns - 37' )
- 19 Buchanan (Kirk - 55' )
- 30 Goodfellow
- 39 Young
- 17 Burns
- 22 Willis
- 24 Hutton
- 10 Kirk
- 12 McDougall
Live Text Commentary
Full Time The game is over, as the referee blows his whistle.90:00 +1:09
Cillian Sheridan produces a right-footed shot from the edge of the area and hits the post.90:00 +0:37
Effort from the edge of the area by James Keatings goes wide of the right-hand post.89:37
Chris Smith produces a cross.88:15
Unfair challenge on Chris Millar by Ryan Thomson results in a free kick. Free kick taken by Frazer Wright.87:13
Unfair challenge on James Keatings by Joe Cardle results in a free kick. Indirect free kick taken by David MacKay.86:21 Substitution
Substitution James Keatings on for Lee Croft.85:03
Free kick awarded for an unfair challenge on Cillian Sheridan by Gary Mason. Free kick taken by Alan Mannus.84:06
Effort on goal by Joe Cardle from just inside the penalty area goes harmlessly over the target.83:46
The ball is delivered by Paul Willis.82:35
Martin Hardie is flagged offside by the assistant referee. Indirect free kick taken by Alan Mannus.81:42
The ball is sent over by Paul Burns.77:31
Assist by Murray Davidson.77:31 Goal scored
Goal! - Lee Croft - St J'stone 3 - 1 Dunf'mline Lee Croft fires in a goal from close range to the bottom right corner of the goal. St Johnstone 3-1 Dunfermline.77:18
Liam Craig takes a shot. Save by Chris Smith.75:12 Substitution
Substitution Marcus Haber replaces Francisco Sandaza.74:20
Francisco Sandaza produces a left-footed shot from outside the box and misses left.73:40
The ball is delivered by Joe Cardle, clearance by Callum Davidson.72:18 Goal scored
Goal! - Paul Burns - St J'stone 2 - 1 Dunf'mline Goal scored by Paul Burns from just inside the penalty area to the bottom left corner of the goal. St Johnstone 2-1 Dunfermline.72:07
Joe Cardle sends in a cross, clearance by Frazer Wright.
Corner taken by Joe Cardle. Inswinging corner taken by Joe Cardle, Alan Mannus makes a save.68:59
Lee Croft takes a shot.68:27
Unfair challenge on Callum Davidson by Ryan Thomson results in a free kick. Alan Mannus takes the free kick.67:36
The ball is swung over by Joe Cardle.66:47
Free kick awarded for a foul by David McCracken on Martin Hardie. Austin McCann takes the indirect free kick. A cross is delivered by Paul Willis.65:01
Austin McCann takes a shot. Inswinging corner taken by Joe Cardle.62:30
Murray Davidson takes a shot. Save by Chris Smith.61:50
Francisco Sandaza produces a cross.60:19
The official flags Joe Cardle offside. Alan Mannus takes the free kick.59:55
Unfair challenge on Martin Hardie by David McCracken results in a free kick. Austin McCann takes the indirect free kick.59:03
Paul Burns challenges Liam Craig unfairly and gives away a free kick. Frazer Wright restarts play with the free kick.58:30
Callum Davidson sends in a cross.57:30
Free kick awarded for a foul by Chris Millar on Paul Burns. Andy Dowie takes the free kick.54:23 Substitution
Substitution Andy Kirk is brought on as a substitute for Liam Buchanan.53:35
Paul Willis has an effort at goal from just inside the box that misses to the right of the goal.52:13
Lee Croft produces a cross.51:39
Murray Davidson takes a shot. Clearance made by Alex Keddie.49:15
Martin Hardie gives away a free kick for an unfair challenge on Murray Davidson. Free kick taken by David MacKay.48:15
The ball is swung over by Cillian Sheridan, save made by Chris Smith.46:14
The assistant referee signals for offside against Cillian Sheridan. Free kick taken by Andy Dowie.45:01
The game restarts for the second half.45:01 Substitution
Substitution Patrick Boyle goes off and Paul Willis comes on.45:00 +1:03 Half time
Half Time The referee blows for half time.43:47
Murray Davidson fouled by Ryan Thomson, the ref awards a free kick. Free kick taken by Liam Craig.42:06
David MacKay produces a right-footed shot from just outside the penalty box that goes wide left of the target.41:49
Centre by Joe Cardle, Alan Mannus makes a save.36:13 Substitution
Substitution Paul Burns comes on in place of David Graham.34:19
The assist for the goal came from Francisco Sandaza.34:19 Goal scored
Goal! - Callum Davidson - St J'stone 2 - 0 Dunf'mline A goal is scored by Callum Davidson from just inside the penalty area to the bottom right corner of the goal. St Johnstone 2-0 Dunfermline.34:15
The ball is delivered by Callum Davidson.32:44
Francisco Sandaza provided the assist for the goal.32:44 Goal scored
Goal! - Murray Davidson - St J'stone 1 - 0 Dunf'mline Murray Davidson fires in a goal from just inside the area to the bottom left corner of the goal. St Johnstone 1-0 Dunfermline.32:06
Unfair challenge on Chris Millar by Martin Hardie results in a free kick. Chris Millar takes the indirect free kick.31:44
Murray Davidson takes a shot. Chris Smith makes a save.30:13
Lee Croft takes a shot. Save by Chris Smith.27:08
Liam Craig concedes a free kick for a foul on Martin Hardie. Free kick crossed right-footed by Andy Dowie, save by Alan Mannus.24:28
Free kick awarded for a foul by Austin McCann on Francisco Sandaza. Liam Craig takes the free kick. Corner taken by Lee Croft, Chris Smith makes a save.19:11
Unfair challenge on Frazer Wright by Austin McCann results in a free kick. Alan Mannus takes the free kick.16:13
Liam Craig takes a inswinging corner. David McCracken takes a shot. Blocked by Patrick Boyle.15:17
David Graham delivers the ball, clearance made by David MacKay.14:22
Lee Croft takes a shot. Chris Smith makes a save.12:45 Substitution
Substitution Chris Millar comes on in place of Jody Morris.11:41
Centre by Andy Dowie, clearance made by David McCracken.10:58
David MacKay produces a cross, Alex Keddie makes a clearance.9:18
Frazer Wright takes a shot.4:59
Jody Morris takes a shot. Inswinging corner taken right-footed by Lee Croft from the left by-line, Murray Davidson takes has a header from just inside the penalty box which clears the crossbar.3:25
Austin McCann concedes a free kick for a foul on Francisco Sandaza. Direct free kick taken by Jody Morris. The ball is sent over by Lee Croft.0:00
The game gets underway.
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