A Luke Williams effort separated the sides until added time when Mustapha Carayol's 12-yard effort made sure of the points.
Boro had the better of the early exchanges but Paul Jewell's side never gave up.
The home side went close after just five minutes when a foul by Michael Chopra on Williams gave the hosts a free-kick wide on the right.
Adam Reach took it and Ishmael Miller's header from 12 yards out was cleared by Aaron Cresswell.
The dangerous Miller came even closer to breaking the deadlock four minutes later when his close-range shot was beaten out by Ipswick keeper Scott Loach.
The visitors were firmly on the back foot early on but made their presence felt after 13 minutes when an inswinging corner from Adam Drury was met by Tommy Smith who forced a save from Jason Steele in the Boro goal.
Paul Taylor and Cresswell went close from distance as Jewell's side achieved territorial parity, and after 25 minutes Chopra's right-footed effort from 18 yards needed to be blocked by Boro's Andre Amougou.
The Tractor Boys went close again two minutes later when a cross by Taylor was tipped over by Steele and from the resulting corner by Drury, Steele was brought into action again to save Smith's close-range header.
But having battled back from Boro's fine start, the visitors found themselves a goal down against the run of play after 34 minutes when Williams shot home from the edge of the penalty area to give Tony Mowbray's men the lead.
Boro went close to doubling their advantage four minutes later when George Friend's shot from 20 yards brought a hasty clearance from Luke Chambers.
Mowbray's men picked up where they had left off after the break and Miller's 12-yard effort forced a save from Loach.
Miller, who had taken a knock, was replaced by Lukas Jutkiewicz after 56 minutes and the replacement went close to adding to Boro's tally within four minutes when his left-footed effort was just wide.
But while Boro looked the more threatening side, the Tractor Boys could not be discounted and Steel was forced into action again after 67 minutes when Chopra's right-footed effort from 12 yards was only parried to safety by the Boro keeper.
Ipswich looked threatening and Boro were forced onto the defensive to protect their slender lead as Taylor's 25-yard effort fizzed wide with 15 minutes left.
The visitors continued to press with Carlos Edwards and Taylor in particular looking threatening in the closing stages.
But Carayol had the final word as the home side rode their luck for maximum points.