The visitors were 3-0 up after just 48 minutes and although Town fought back strongly they only managed a solitary consolation.
Ipswich's poor defending again proved costly, but they weren't helped by injuries to starting central defensive pair Georges Santos and Drissa Diallo, who both went off injured before half-time.
Both keepers were forced into early action - Andy Marshall, on loan from Ipswich, caught a Shefki Kuqi header, before Kelvin Davis parried a fierce Mark McCammon drive.
Diallo and McCammon both went off after a clash of heads and it was the Millwall man's replacement who opened the scoring on 30 minutes, Neil Harris smashing in from a Danny Dichio flick.
Town's poor marking was in evidence then, and cost them again on 37 minutes when Darren Ward rose unmarked to flick in a Harris cross.
Any hopes of an Ipswich comeback were all but ended on 48 minutes when Harris flicked on a Tim Cahill cross, and although Davis palmed it on to the bar, the linesman correctly ruled the ball had crossed the line.
Ipswich did get one goal back on 53 minutes when half time sub Dean Bowditch's low cross found Darren Bent who slotted home.
That sparked a sustained spell of Town pressure, but Marshall denied Bowditch and Tommy Miller, Martijn Reuser flashed a 20-yard drive just wide and Jim Magilton headed wide when unmarked from a Reuser free-kick.
Although Town continued to press, Millwall held out fairly comfortably after that, but they should have had a penalty given against them late on when Kevin Muscat appeared to bodycheck Bowditch in the area, but ref Mike Riley capped an erratic display by booking the Town man for a dive.