Jake Cooper’s 27th-minute goal has given Millwall a 1-0 lead over the Blues at Portman Road at half-time.
Mustapha Carayol, Bersant Celina, Stephen Gleeson and Myles Kenlock returned to the Blues’ starting line-up with Town lining up in a 3-4-3 system.
Jonas Knudsen replaced Cameron Carter-Vickers, who dropped to the bench, in the back three with Adam Webster moving to the right.
Kenlock was the left wing-back with Jordan Spence on the right and Cole Skuse in the centre of midfield with Gleeson. Celina and Carayol were up front with Martyn Waghorn.
Millwall, who are unchanged from Friday's 2-0 home victory over Nottingham Forest, included former Blues loanee Ryan Tunnicliffe on the bench.
After a minute’s applause for former coach and manager Bobby Ferguson and ex-player Colin Harper, who both died last week, Town started brightly and felt they should have been awarded a penalty in the third minute when Waghorn was shoved over in the area by Cooper.
It looked far more of a penalty than the one Birmingham were given on Saturday but referee Stephen Martin waved away the protests.
In the 10th minute a cross-field ball from Webster from the right found Waghorn at the far post but Jordan Archer twice saved from close range and the ball cannoned behind off the Town striker.
Millwall threatened for the first time in the 12th minute when Lee Gregory got a loose ball under control in the area and hit a shot which deflected wide off a Town player.
But the Blues had played some good stuff in the early stages, keeping the ball far better than in most recent games, and a minute later Celina fed Skuse on the right of the box. The midfielder cut across but Cooper bundled behind.
Just after the quarter of an hour mark Bialkowski twice found himself in trouble as he looked to kick.
First Chambers over-hit a backpass which the Polish international was able to scamper back and clear. Then, moments later, the Blues keeper dallied on the ball and allowed Steve Morison to dispossess him before grabbing it. The Millwall skipper tried to kick it out of his hands and was penalised by referee Martin.
Carayol came within a couple of inches of a brilliant first home goal for the Blues in the 24th minute, cutting in from the left before smashing a powerful shot just over the bar.
However, it was the visitors who took the lead in the 27th minute. Following a freekick which had been cleared, Ben Marshall crossed from the left and Jake Cooper stepped back off his man to nod a header past Bialkowski.
Two minutes after going behind Waghorn hit a low freekick from the right round the Millwall wall but too far in front of a number of on-rushing Town players and keeper Archer was able to claim.
The Lions should have doubled their lead in the 34th minute when Gregory crossed low from the right to the far post but George Saville was unable to keep the ball down as he slid in.
Millwall had been firmly in control having gone in front and a minute later Gregory crossed from the left and Morison flicked his header across the face and wide. Neither side created another opportunity before referee Martin brought the half to a close.
Town had started well with attacking trio Waghorn, Carayol and Celina presenting a threat. The Blues had looked the more likely scorers until Millwall went in front having looked dangerous from earlier set pieces.
The Lions, looking for a club record seventh successive Football League away win, took charge from there and had chances to extend their lead with the Blues not threatening to get on terms.
Town: Bialkowski, Webster, Chambers (c), Knudsen, Spence, Skuse, Gleeson, Kenlock, Celina, Carayol, Waghorn. Subs: M Crowe, Connolly, Ward, Hyam, Sears, Carter-Vickers, Folami.
Millwall: Archer, Meredith, Hutchinson, Williams, Gregory, Romeo, Wallace, Morison (c), Saville, Cooper, Marshall. Subs: Martin, Tunnicliffe, Cahill, Onyedinma, Elliott, O’Brien, Shackell. Referee: Stephen Martin (Staffordshire).