Town got back on track in the Championship with an early goal from Jason Scotland and a penalty from Grant Leadbitter giving Roy Keane's side the three points.
Scotland took his tally for the season to five goals - all at Portman Road - with a fifth minute strike after Millwall had failed to deal with a cross.
Tommy Smith and Jack Colback went close to adding to the lead before Leadbitter converted from the spot after Danny Shittu was judged to have fouled Tamas Priskin in the box early in the second-half.
Town made two changes to the side that beat Northampton in the Carling Cup, Marton Fulop and Colback returning to the side with Brian Murphy and Andros Townsend dropping to the bench.
Priskin hit the sidenetting inside the first minute before Scotland gave Blues the perfect start soon after, taking advantage of Paul Robinson failing to clear Carlos Edwards' cross - the Trinidad and Tobago international finding the net from 10 yards.
Gareth McAuley cleared the danger from Alan Dunne's cross as Millwall responded, Steve Morison's winding run ended by Tom Eastman's intervention.
Fulop saved comfortably from James Henry's right foot effort, Morison then shooting over the bar as the Lions continued to threaten.
Damien Delaney diverted Henry's dangerous cross behind for a corner, then it took a great tackle from Eastman to prevent Theo Robinson getting on the end of Scott Barron's cross.
Former Blue Barron was finding space down the Millwall left with his willingness to join the attack and from another cross, McAuley held firm to clear from Morison.
Millwall had a penalty claim after the ball hit Leadbitter's arm but referee Kevin Friend rightly waved away the Lions' claims, Danny Schofield forcing McAuley to clear for a corner as the visitors pressed for an equaliser.
Town came closest to adding to the lead in the 10 minutes before the break, Delaney sending a header wide from a great position following a corner, Leadbitter seeing his shot deflected over after a clever free-kick with Colback and from the resultant corner, Smith powered a header goalwards that was cleared off the line by Henry.
Millwall continued to create chances though and the half finished with Robinson heading over from Nadjim Abdou's cross.
Town had a gilt edged chance to extend the advantage three minutes after the restart, Edwards sending Colback clear on goal but the Sunderland loanee's strike went inches wide.
Millwall made a first change on 54 minutes, a double swap with Darren Carter on for Abdou and Robinson making way for John Marquis.
A minute later Town were two ahead, Priskin judged to have been blocked as he turned inside Shittu and Leadbitter converted his second penalty of the season.
Henry lashed a left foot shot well over for the Lions after former Blue Liam Trotter had tried to find space on the edge of the Blues' box.
David Forde saved well from Scotland after David Norris had put the striker through on goal, the Lions' keeper holding firm from Leadbitter's long range shot as
Town threatened to wrap up the points before the hour.
Connor Wickham, back after an ankle injury kept him out of the Northampton game, entered the fray midway through the second-half, Priskin receiving warm applause from the home fans as he made way.
McAuley was in the right place again to deny Marquis inside the Town box as Millwall searched for a way back into the game, Henry's cross then flashing across goal.
Blues made a second change with Ronan Murray replacing Scotland for the final 20 minutes, leaving Blues with a teenage spearhead - the 19-year-old joining 17-year-old Wickham in attack, Jake Livermore replacing the injured Norris soon after.
Delaney went close to a second goal in successive games, his header hitting the bar from Edwards' long throw but Millwall still carried a threat and it needed goalline clearances from Smith and McAuley to preserve the lead.
Alan Dunne was booked for a foul on Wickham as the England U19 international looked to get in on goal and Town should have made it three in added on times, Wickham's shot beaten out by Forde and from the follow up Livermore hit the post and then sent the rebound over the bar.
It mattered not as Blues ended a run of three straight defeats in the Championship to push back up towards the top six.
Town: Fulop, Eastman, McAuley, Delaney, Smith, Edwards, Leadbitter, Norris (Livermore 80), Colback, Priskin (Wickham 65), Scotland (Murray 70). Subs not used: Murphy, Peters, Townsend, Brown.
Millwall: Forde, Dunne, Robinson, Shittu, Barron, Henry, Trotter, Abdou (Carter 53), Schofield, Robinson (Marquis 53), Morison. Subs not used: Mildenhall, Hackett, Craig, Ward, Laird. Booked: Dunne