Whilst manager Dennis Wise will welcome the points earned against a below par Town, he will rue the fact that he will be without both Darren Ward and Paul Ifill who he lost to injury with games against Derby Rotherham and Watford coming up in the next week.
Wise could not have complained if his Ipswich had gone into the break with a sizeable lead, but were frustrated by a combination of poor finishing and good goalkeeping.
Darren Bent and Shefki Kuqi looked dangerous, but were guilty of missing a string of good chances and Ipswich had their penalty claims waved away by referee Paul Armstrong as Tommy Miller went down under pressure from David Livermore.
Bent was sent clear by Kuqi midway through the half, but Andy Marshall was quick off of his line and saved well with his legs at the feet of the England under-21 striker.
Despite Ipswich's domination it was the home side who took the league through Barry Hayles with a looping shot from 25-yards deep into first half injury time.
As the visitors failed to clear their defences the ball fell kindly to the former Fulham striker and he chipped Kelvin Davis with a superb finish for his 4th goal of the season.
The goal stunned the visitors and they were clearly still feeling the effects after the break when the went 2-0 down on 48 minutes.
Marvin Elliot crossed the ball into the box which fell to the feet of an un-marked Danny Dichio as Ipswich got their off-side trap all wrong and the striker was left an easy tap in from just six yards.
Millwall should have a had a third when Hayles beat the off-side trap again, but was denied by a superb last ditch block from Fabian Wilnis.
Ipswich clawed one back just after the hour when Kuqi diverted Tommy Miller's shot into the back of the net with a cheeky back-heel flick that left Marshall no chance.
But it was in vain as Scott Dobie sealed the victory as Ipswich's offside trap again failed allowing Dobie break clear and, with just Kelvin Davis left to beat, slot the ball home with a cool finish.