While player-manager Dennis Wise will welcome the points he will rue the fact that he will be without both Darren Ward and Paul Ifill as they face Derby County, Watford and then Rotherham United in the next week.
He could not have complained if Ipswich had gone into the break with a sizeable lead, but the visitors were frustrated by a combination of poor finishing and good goalkeeping.
Marcus Bent and Shefki Kuqi looked dangerous, but were guilty of missing a string of good chances and Ipswich had 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 that took the lead through Barry Hayles with a looping 25-yard shot deep into first-half stoppage time.
As the visitors failed to clear, the ball fell kindly to the former Fulham striker and he chipped Kelvin Davis with a superb finish for his fourth goal of the season.
The goal stunned the visitors and they were clearly still feeling the effects after the break when they went 2-0 down in the 48th minute.
Marvin Elliott's cross fell to the feet of the unmarked Danny Dichio as Ipswich got their offside trap all wrong and the striker was left with an easy tap-in from just six yards.
Millwall should have a had a third when Hayles beat the offside 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 net with a cheeky back-heel that gave Marshall no chance.
But it was all in vain as Scott Dobie sealed the victory as Ipswich's offside trap again failed and he beat Davis with a cool finish.