Michael Chopra's first-half goal gave Ipswich victory and piled on the misery for crisis club Portsmouth, who applied for administration earlier on Tuesday.
Ipswich's Damien Delaney hit the bar with a header after just five minutes.
Chopra then broke the deadlock, reacting quickest when Daryl Murphy nodded against the post.
The home side got the ball in the net after the break from Greg Halford's long throw, but referee Darren Deadman ruled that no-one else had touched it.
Portsmouth boss Michael Appleton felt the goal should have stood, because he felt Ipswich's Jay Emmanuel-Thomas touched the ball on its way in.
Pompey's financial problems mean a 10-point penalty is imminent - which would leave Michael Appleton's side 21st in the Championship and above the relegation zone only on goal difference.
They got off to a terrible start on the field too, and had to survive a wave of Ipswich attacks straight from kick-off.
Delaney's header skimmed the bar, Pompey keeper Stephen Henderson almost spilled a Jay Emmanuel-Thomas shot, and a Martin free-kick fizzed over.
Ipswich did take the lead on 13 minutes when Murphy's header hit the woodwork and the ball fell for Chopra to nudge it over the line for his 11th goal of the season and fourth in the last three games.
Pompey's fans had turned out in force to lift their side but they had precious little to encourage them.
Futacs almost levelled against the run of play when he made the most of a defensive error to take a shot that was deflected wide.
In the meantime, Ipswich were still pouring forward and should have extended their lead.
Martin fired over from an Andy Drury pull-back, before Drury himself fired wide, and the same two players were denied again late on when Martin hit the post and Henderson denied Drury.
The result was never in doubt, though, despite those Pompey claims for a goal.
After a run of two wins in 16 games, Paul Jewell's side have now won their last three matches to climb above Pompey to 17th in the table.
VIEWS FROM THE DRESSING ROOM
Portsmouth boss Michael Appleton:
"I hope the referee is disappointed with the decision he made. I was so disappointed for the fans because they came in their droves and it would have been nice to get something out of the game for them.
"Basically Emmanuel-Thomas kneed the ball into his own goal. I thought it was a goal right away because the ball changed angles as it went into the back of the net.
"The boy knew as well. You could tell in his face that he had scored an own goal."
Ipswich Town manager Paul Jewell:
"It was a difficult night to come here with everything that's going on at this football club. It's obviously a tough time for everyone connected to it and especially the supporters.
"We knew they would be as one, back their team and we knew we had to start quick and not let them get any momentum. We started the game very fast and very sharp. The goal was the least we deserved.
"On the balance of play, I think we fully deserved to win. On paper, it may be a 1-0, but we could have scored four or five."
Full Time The game is over, as the referee blows his whistle.
The ball is swung over by Joel Ward, clearance made by Damien Delaney.
Andy Drury challenges Tal Ben-Haim unfairly and gives away a free kick. Stephen Henderson takes the direct free kick.
Lee Martin decides to take a short corner.
The ball is crossed by Erik Huseklepp.
90:00 +1:10 Substitution
Substitution Adam Webster replaces Greg Halford.
Lee Martin takes a shot from 35 yards and missed to the left of the net.
The ball is delivered by Aaron Cresswell, Stephen Henderson makes a comfortable save.
Dave Kitson is penalised for handball and concedes a free kick. Direct free kick taken by Aaron Cresswell.
Jason Scotland takes a shot. Jason Pearce gets a block in.
Effort from inside the six-yard box by Tal Ben-Haim goes wide left of the target.
Lee Martin has an effort at goal from just outside the box which goes wide of the left-hand upright.
Greg Halford delivers the ball, save by Arran Lee-Barrett.
The ball is sent over by Joel Ward.
Andy Drury takes the direct free kick.
Booking Ricardo Rocha receives a yellow card.
Foul by Ricardo Rocha on Daryl Murphy, free kick awarded.
Inswinging corner taken right-footed by Erik Huseklepp from the left by-line to the near post.
Substitution Benjani Mwaruwari on for Kelvin Etuhu.
Substitution (Ipswich) makes a substitution, with Jason Scotland coming on for Michael Chopra.
Outswinging corner taken by Lee Martin from the right by-line, Daryl Murphy takes a shot. Save made by Stephen Henderson. Inswinging corner taken by Lee Martin, Damien Delaney has a header from close range and clears the crossbar.
Lee Martin has an effort from just inside the box that misses to the left of the target.
Andy Drury takes a outswinging corner to the near post, Kelvin Etuhu manages to make a clearance.
The ball is sent over by Daryl Murphy.
The assistant referee signals for offside against Michael Chopra. Stephen Henderson takes the indirect free kick.
Andy Drury takes a inswinging corner.
Effort from inside the area by Andy Drury misses to the right of the target.
The ball is delivered by Daryl Murphy, Effort on goal by Lee Martin from deep inside the area goes harmlessly over the bar.
A cross is delivered by Kelvin Etuhu, Dave Kitson has an effort at goal from just inside the box that misses to the right of the goal.
Michael Chopra is ruled offside. Indirect free kick taken by Tal Ben-Haim.
Outswinging corner taken by Andy Drury, save by Stephen Henderson.
Effort from the edge of the area by Marko Futacs goes wide of the right-hand post.
The referee blows for offside against Dave Kitson. Free kick taken by Arran Lee-Barrett.
Michael Chopra concedes a free kick for a foul on Ricardo Rocha. Direct free kick taken by Stephen Henderson.
Aaron Cresswell delivers the ball.
Kelvin Etuhu produces a cross.
Tal Ben-Haim restarts play with the free kick. The ball is crossed by Erik Huseklepp, Andy Drury manages to make a clearance.
Booking Damien Delaney receives a caution for unsporting behaviour.
Damien Delaney concedes a free kick for a foul on Dave Kitson.
Jason Pearce gives away a free kick for an unfair challenge on Lee Martin. Carlos Edwards takes the direct free kick.
Shot from just outside the box by Joel Ward misses to the left of the target.
Jay Emmanuel-Thomas has an effort direct from the free kick.
Jay Emmanuel-Thomas takes the free kick.
Booking Greg Halford booked for unsporting behaviour.
Lee Martin fouled by Greg Halford, the ref awards a free kick.
The ball is crossed by Erik Huseklepp.
Unfair challenge on Carlos Edwards by Dave Kitson results in a free kick. Arran Lee-Barrett takes the free kick.
Tommy Smith concedes a free kick for a foul on Dave Kitson. Direct free kick taken by Dave Kitson.
The referee gets the second half started.
45:00 +3:03 Half time
Half Time The referee blows for half time.
Free kick awarded for an unfair challenge on Tal Ben-Haim by Daryl Murphy. Tal Ben-Haim takes the free kick.
Aaron Cresswell crosses the ball.
Andy Drury crosses the ball, clearance made by Jason Pearce.
Substitution Dave Kitson is brought on as a substitute for Liam Lawrence.
Andy Drury takes a shot. Stephen Henderson makes a save.
A cross is delivered by Daryl Murphy.
Long range effort from Andy Drury misses to the left of the goal.
Marko Futacs takes a shot. Arran Lee-Barrett makes a comfortable save.
Direct free kick taken by Stephen Henderson.
Booking Jay Emmanuel-Thomas booked.
Free kick awarded for a foul by Damien Delaney on Jason Pearce.
Liam Lawrence concedes a free kick for a foul on Lee Martin. Free kick taken by Aaron Cresswell.
Hayden Mullins takes a shot. Blocked by Damien Delaney.
Liam Lawrence takes the free kick.
Booking Booking for Luke Hyam for unsporting behaviour.
Luke Hyam gives away a free kick for an unfair challenge on Ricardo Rocha.
The referee blows for offside against Erik Huseklepp. Free kick taken by Arran Lee-Barrett.
Marko Futacs takes a shot. Save by Arran Lee-Barrett. Inswinging corner taken right-footed by Liam Lawrence played to the near post, Ricardo Rocha has a header from close range and clears the crossbar.
Lee Martin is adjudged to have handled the ball. Free kick taken by Liam Lawrence.
Michael Chopra takes a shot. Blocked by Tal Ben-Haim.
Luke Hyam challenges Kelvin Etuhu unfairly and gives away a free kick. Liam Lawrence takes the free kick.
Unfair challenge on Liam Lawrence by Lee Martin results in a free kick. Jason Pearce takes the free kick.
Free kick awarded for a foul by Andy Drury on Liam Lawrence. Jason Pearce takes the free kick.
Free kick awarded for an unfair challenge on Liam Lawrence by Lee Martin. Free kick taken by Tal Ben-Haim.
Free kick awarded for a foul by Liam Lawrence on Andy Drury. Direct free kick taken by Aaron Cresswell.
Assist on the goal came from Damien Delaney.
12:17 Goal scored
Goal - Michael Chopra - Portsmouth 0 - 1 Ipswich Michael Chopra finds the back of the net with a headed goal from inside the six-yard box. Portsmouth 0-1 Ipswich.
Free kick taken by Arran Lee-Barrett.
Booking Booking for Tal Ben-Haim.
Tal Ben-Haim concedes a free kick for a foul on Aaron Cresswell.
Centre by Daryl Murphy, blocked by Tal Ben-Haim. Andy Drury decides to take a short corner.
The ball is sent over by Daryl Murphy, Tal Ben-Haim gets a block in. Liam Lawrence decides to take the corner short.
Foul by Tal Ben-Haim on Aaron Cresswell, free kick awarded. Direct strike on goal from the free kick comes in from Lee Martin.
Michael Chopra takes a shot. Save by Stephen Henderson.
Jay Emmanuel-Thomas takes a shot. Save by Stephen Henderson.
Damien Delaney takes a shot.
Foul by Ricardo Rocha on Lee Martin, free kick awarded. Direct free kick taken by Andy Drury.
Corner taken by Andy Drury from the left by-line. Andy Drury takes a short corner.
The game gets underway.
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