Sheffield Wednesday loanee Shefki Kugi won and converted a first-half penalty, before sending Ian Westlake clear to score, while Darren Bent added a late third.
A quiet first period was slow to come to life although Richard Naylor did head a good chance over on six minutes from a Matt Richards cross.
Bent saw an angled shot easily held by Paul Gerrard before putting a Jim Magilton corner over from six yards.
In between United felt they should have had a penalty when home keeper Kelvin Davis caught Jack Lester, but referee Mick Fletcher ruled Lester did not have control of the ball.
Bent put another chance over before Westlake netted after Gerrard could only parry a Magilton shot, but he was ruled offside.
Town went ahead on 43 minutes when Bent's flick put Kuqi in. Chris Morgan pulled him down and Kuqi drilled the penalty beneath the diving Gerrard.
Davis produced a great save early in the second half to deny Lester who looked sure to score after turning onto a Ashley Ward knockdown.
Fine defending by Rob Kozluk put off Bent as he looked set to head home a Magilton cross but Town did double the lead on 67 minutes when Kuqi's lay-off sent Westlake clear to fire past Gerrard.
Bent was foiled by Gerrard, who spent time on loan at Portman Road last season, after the striker raced onto a Magilton throughball, and then substitute Paul Peschisolido had the ball in the net for the Blades, but keeper Davis had been fouled as he came for the ball.
Bent finally got the goal he deserved when he converted a low Westlake cross in the final minute.