Boosted by a six-point Easter, Joe Royle's men were clear favourites against inconsistent Gillingham whose poor home form is a big reason why they could be relegated.
This was their 11th loss in front of their own fans this season, in a game of two contrasting halves, with the Gills dominating much of the first and Ipswich bossing the second.
Royle had to draft in untried goalkeeper Lewis Price for a shock first-team debut. The Welsh Under-19 international got his chance after Kelvin Davis pulled out with a stomach bug in the morning.
Price's first real job was to face an eighth minute penalty by John Hills, given when Patrick Agyemang went down in the area under a challenge from Matt Elliott.
Hills stepped up to convert the penalty, Gillingham's first success from the spot in five attempts.
Elliott and his fellow back four looked shaky every time they were tested, and they all received yellow cards before half time.
Matt Richards had a nervous first 20 minutes and was the first to be booked followed by Elliott, John McGreal with Fabian Wilnis completing the quartet just before the break.
By then, Royle and assistant Willie Donachie had started to ring the changes. They pulled off Shefki Kuqu in favour of Richard Naylor and Ipswich started to improve.
Naylor, Darren Bent and Ian Westlake all went close but Gillingham went in at the break 1-0 up.
Wilnis was replaced by Drissa Diallo during the interval, but the most telling change involved the introduction of Martijn Reuser.
He replaced the limping Tommy Miller and immediately began to have a major say in the game.
His 62nd minute free-kick put Ipswich level, and then five minutes later he got down the left to fire in the perfect cross which Bent headed in for the eventual winner.
Ipswich lost 4-3 to the Gills at Portman Road earlier this season and their 42 previous games had included a total of 146 goals.
Bent was close to a 147th but saw his excellent drive come back off a post as Ipswich moved closer to a place in the play-offs.