A debut goal from French midfielder Bakary Sako earned Wolves a Capital One Cup third-round trip to Chelsea.
The 24-year-old, who joined the club from St Etienne on Wednesday, fired in from 20 yards in stoppage time.
Central defender Danny Batth had scrambled in a 16th-minute goal for the visitors, but boyhood Wolves fan Clive Platt equalised.
Frank Nouble restored Wolves' lead in first-half injury time with another scruffy goal, before Sako struck.
Wolves have been inconsistent in the Championship this season, collecting four points from three games, but were largely in control against their League Two opponents.
After a lively start by the home side, Batth bundled in his first goal for Wolves from Razak Boukari's corner.
Northampton had knocked out last season's finalists Cardiff in the first round, but rarely threatened the Wolves goal until they equalised five minutes before half-time.
Veteran striker Platt, 34, scored it by climbing above Batth to head in Chris Hackett's right-wing cross.
Wolves regained the lead in first-half stoppage time when Anthony Forde headed back a Boukari cross and Nouble saw the ball bounce up off his chest and creep over the line for his first Wolves goal.
Boukari, who had an impressive debut on the right wing after joining from Rennes on Monday, saw a shot blocked by Kelvin Langmead early in the second half after keeper Dean Snedker spilled a cross.
The 17-year-old keeper, making only his second senior appearance, then dived at the feet of Wolves midfielder David Davis, who had been put through by Boukari.
Sako replaced the Togo international midway through the second half, and thumped in a third goal late on.
VIEW FROM THE DRESSING ROOM
Northampton Town manager Aidy Boothroyd told BBC Northampton:
"All I hoped was that the players would give their all and leave nothing on the pitch.
"The manner we conceded the goals was poor but we've got a young boy in goal and he'll get better and better.
"They were sloppy, flukey goals. We had the better chances but that's the quality you're playing against.
"We take it on the chin, say good luck to Wolves in the next round and we concentrate on our league form which is very important for us."
- 13 Snedker
- 03 Widdowson
- 05 Langmead
- 12 Tozer (Akinfenwa - 57' )
- 18 Artell
- 23 East
- 04 Guttridge
- 08 Harding
- 11 Hackett
- 09 Platt (Moult - 73' )
- 14 Nicholls (Mukendi - 46' )
- 26 Heath
- 06 Charles
- 07 Demontagnac
- 10 Akinfenwa
- 15 Mukendi
- 16 Wilson
- 19 Moult
- 13 Ikeme
- 03 Elokobi
- 05 Stearman
- 25 Batth
- 34 Margreitter
- 17 Boukhari (Sako - 67' )
- 22 Jonsson Booked (Doumbia - 67' )
- 26 Davis
- 27 Forde (Peszko - 83' )
- 15 Sigurdarson
- 18 Nouble
- 36 McCarey
- 16 Berra
- 30 Doherty
- 07 Peszko
- 10 Sako
- 19 Hammill
- 28 Doumbia
Live Text Commentary
Full Time The referee blows for the end of the match.90:00 +0:56
Assist by Slawomir Peszko.90:00 +0:56 Goal scored
Goal! - Bakary Sako - Northamp'n 1 - 3 Wolves Bakary Sako finds the back of the net with a goal from outside the penalty box to the bottom left corner of the goal. Northampton 1-3 Wolverhampton.90:00 +0:31
Long range effort by Kelvin Langmead goes wide right of the target.89:47
Bjorn Sigurdarson challenges Danny East unfairly and gives away a free kick. Dean Snedker takes the direct free kick.89:15
Louis Moult takes a shot. Save made by Carl Ikeme.88:53
The ball is swung over by Bakary Sako, clearance made by David Artell.86:41
Bjorn Sigurdarson has an effort at goal from outside the penalty box missing to the wide right of the target.85:57
Kelvin Langmead is caught offside. Danny Batth restarts play with the free kick.84:16
Centre by Bjorn Sigurdarson, Shot from 12 yards from Slawomir Peszko. David Artell gets a block in. Corner taken left-footed by Bakary Sako, Dean Snedker makes a save.83:28
Foul by Adebayo Akinfenwa on Tongo Doumbia, free kick awarded. Direct free kick taken by Bakary Sako.82:35 Substitution
Substitution (Wolverhampton) makes a substitution, with Slawomir Peszko coming on for Anthony Forde.77:06
Chris Hackett produces a left-footed shot from outside the penalty box and misses left.75:19
Anthony Forde delivers the ball.74:35
Henoc Mukendi crosses the ball, clearance by Georg Margreitter.72:47 Substitution
Substitution Louis Moult comes on in place of Clive Platt.72:25
A cross is delivered by Bakary Sako, clearance by David Artell.70:30
Chris Hackett crosses the ball, clearance by Georg Margreitter.69:22
Anthony Forde takes a shot. Save by Dean Snedker.67:47
George Elokobi delivers the ball, Kelvin Langmead manages to make a clearance.
Substitution Tongo Doumbia replaces Eggert Jonsson.66:01 Substitution
Substitution Bakary Sako is brought on as a substitute for Razak Boukari.65:41
Razak Boukari has an effort at goal from just inside the box that misses to the right of the target.64:04
The ball is sent over by Chris Hackett, clearance by Georg Margreitter.62:45
Ben Harding takes a inswinging corner from the right by-line to the near post, save made by Carl Ikeme.62:21
Ben Harding takes a shot. Danny Batth gets a block in.61:54
Anthony Forde takes a shot. Bjorn Sigurdarson gets a block in.60:14
Right-footed shot by Razak Boukari missed to the left of the target.57:09
The ball is sent over by Henoc Mukendi, Adebayo Akinfenwa challenges Richard Stearman unfairly and gives away a free kick. Carl Ikeme restarts play with the free kick.56:19 Substitution
Substitution Adebayo Akinfenwa on for Ben Tozer.54:16
Chris Hackett takes a shot. Carl Ikeme makes a save.54:01
Eggert Jonsson gives away a free kick for an unfair challenge on Clive Platt. Clive Platt restarts play with the free kick.52:31
Unfair challenge on Clive Platt by David Davis results in a free kick. Direct free kick taken by David Artell.52:10
Richard Stearman takes a shot. Dean Snedker makes a save.50:57
Anthony Forde takes a inswinging corner.50:42
Corner taken right-footed by Anthony Forde.50:22
David Davis takes a shot. Save by Dean Snedker.50:03
Frank Nouble takes a shot. Blocked by Dean Snedker.49:48
The ball is crossed by George Elokobi, save by Dean Snedker.48:23
Ben Tozer fouled by Eggert Jonsson, the ref awards a free kick. Free kick taken by Kelvin Langmead.47:09
Bjorn Sigurdarson takes a shot. David Artell gets a block in.46:37
Richard Stearman has an effort at goal from close range which goes wide left of the target.45:01
The referee gets the second half started.45:01 Substitution
Substitution Henoc Mukendi on for Alex Nicholls.45:00 +2:14 Half time
Half Time The referee blows for half time.45:00 +1:48
Chris Hackett concedes a free kick for a foul on George Elokobi. George Elokobi takes the direct free kick.45:00 +0:22
Assist on the goal came from Anthony Forde.45:00 +0:22 Goal scored
Goal! - Frank Nouble - Northamp'n 1 - 2 Wolves Frank Nouble fires in a goal from close range to the top left corner of the goal. Northampton 1-2 Wolverhampton.45:00
A cross is delivered by Razak Boukari.42:17
Direct free kick taken by David Artell.42:17 Booking
Booking Eggert Jonsson receives a yellow card for unsporting behaviour.41:59
Free kick awarded for a foul by Eggert Jonsson on Alex Nicholls.39:33
Assist by Chris Hackett.39:33 Goal scored
Goal! - Clive Platt - Northamp'n 1 - 1 Wolves Clive Platt scores a headed goal from deep inside the penalty box. Northampton 1-1 Wolverhampton.37:02
Inswinging corner taken right-footed by Chris Hackett from the left by-line.36:25
Foul by David Davis on Chris Hackett, free kick awarded. Ben Harding crosses the ball from the free kick left-footed from right wing, clearance made by George Elokobi.36:10
Chris Hackett sends in a cross, clearance by Georg Margreitter.35:47
Short corner worked by Ben Harding.28:14
The ball is crossed by Anthony Forde.28:03
The ball is delivered by Anthony Forde, clearance by Joe Widdowson.27:00
Richard Stearman concedes a free kick for a foul on Alex Nicholls. Direct free kick taken by David Artell.25:54
Chris Hackett takes a shot. Save by Carl Ikeme.23:05
Corner taken short by Anthony Forde.22:29
Corner taken by Anthony Forde from the right by-line, clearance by David Artell.20:27
Foul by David Davis on Ben Harding, free kick awarded. David Artell takes the free kick.17:14
The ball is delivered by Chris Hackett.15:55
The assist for the goal came from Anthony Forde.15:55 Goal scored
Goal! - Danny Batth - Northamp'n 0 - 1 Wolves Danny Batth finds the net with a goal from inside the six-yard box to the bottom left corner of the goal. Northampton 0-1 Wolverhampton.15:31
Corner from the left by-line taken by Anthony Forde,13:42
The ball is crossed by Anthony Forde, save by Dean Snedker.12:09
Inswinging corner taken left-footed by Ben Harding from the right by-line to the near post, George Elokobi manages to make a clearance.8:36
Foul by David Davis on Ben Harding, free kick awarded. Strike on goal comes in from Chris Hackett from the free kick.4:42
The ball is delivered by Ben Tozer, Danny Batth manages to make a clearance.4:06
The ball is delivered by Joe Widdowson.3:28
Unfair challenge on George Elokobi by Clive Platt results in a free kick. George Elokobi takes the free kick.1:44
Alex Nicholls has an effort at goal from outside the box which goes wide right of the goal.0:00
The game kicks-off.
Live data and text provided by our data suppliers