TQ Addy opened the scoring with just three minutes on the clock, finishing confidently at the far post after Elliot Thorpe had driven the Hatters youngsters forward from deep inside his own half.
The former Tottenham youngster, making his first appearance in a Luton shirt, picked the ball up midway inside the Town half and carried it into Millwall territory before releasing Conor Lawless, who squared for Addy to side-foot home.
Addy went close to doubling the advantage moments later, before Town keeper Harry Isted was called into action for the first time, diving full length to his left to push away a curling 20-yard free-kick from Sean O’Brien with 20 minutes gone.
The Lions were level four minutes later when Arthur Penney headed home from a left-wing corner, then Isted had to be alert again to keep out efforts from Seb Drozd and Tyrese Briscoe.
As the visitors exerted more pressuer, centre-half Matt Moloney produced a perfectly timed block to prevent O’Brien getting a clean shot in, and Isted was quickly onto the loose ball to deny Briscoe as the Millwall striker looked to pounce.
With half-time approaching, Thorpe crossed for Tyrelle Newton to head back across goal looking for Lawless, but Millwall managed to clear and the sides headed in at the break all-square.
Millwall took a deserved lead in the 54th minute when Briscoe tapped home from almost on the line, and Isted - by far the busier of the two goalkeepers - had to be at his best again to prevent Abdul Malik making it three soon after.
Coach Adrian Forbes took Thorpe off just after the hour, with first-year scholar Jake Burger replacing him.
The Hatters were soon presented with a glorious chance to level, a loose pass across his own area by Millwall keeper Jordan Gillmore intercepted by Addy, who dragged his shot across goal as the visiting stopper sprinted to cover his line.
A deep corner from the left found Lawless lurking at the far post with just over quarter-of-an-hour to go, but the former Reading man screwed his half-volley into the side-netting as another chance to equalise went begging.
The substitute Adam Wedd – on at left-back for injured Avan Jones, with Josh Swan moving to the right – got to the byline and cut a cross right through the Millwall six-yard box, but Newton couldn’t find the finishing touch with the goal at his mercy.
Millwall always looked dangerous, however, and they added a third in injury-time when their trialist substitute finished from inside the box after Isted had pulled off another good save, without reward.
Town: Isted, Jones (Wedd 77), Moloney, Francis-Clarke, Swan; Pettit, Thorpe (Burger 61), Newton, Nicolson, Lawless, Addy.