The hosts took the lead against the run of play in the 19th minute when Paul Furlong powered home his 12th of the season.
But Lewis Grabban nodded in the equaliser six minutes before half-time after Town goalkeeper Dean Brill had missed David Martin's corner.
The visitors came into the game on the back of a 3-0 win over Port Vale and appeared in confident mood as they got off to a positive start.
Zak Whitbread saw a fourth minute header blocked on the line by David Bell after a Martin corner, before Gary Alexander fired over from 20 yards two minutes later following Grabban's pull back.
Chris Perry's clumsy tenth minute challenge saw Martin curl the resulting free-kick just over the bar from the edge of the area.
Luton eventually settled and a dangerous cross from Dean Morgan on the left saw Matt Spring plant an eight-yard header at Rhys Evans in the 16th minute.
A neat Millwall interchange two minutes later saw Marc Laird fluff his free header ten yards out straight at Brill after good work by Grabban and Alexander.
Laird was shown how it should have been done in the 19th minute when Furlong gave Luton the lead, thumping home his header from six yards after another super delivery from Morgan.
The goal lifted the hosts and Bell almost made it 2-0 two minutes later when, after another Morgan cross, his shot beat Evans but not Paul Robinson on the goalline.
The Lions regrouped, however, and Keith Keane's last-ditch challenge halted Grabban in the 35th minute, before Brill instinctively tipped Whitbread's header over after Ali Fuseini's corner a minute later.
It was another corner, this time from Martin, which forced Millwall's leveller in the 39th minute as Brill turned from hero to villain, completely missing the ball and allowing Grabban to nod into the unguarded net.
Jay Simpson started the second half with a 20-yard shot at Brill just seconds in, before Stephen O'Leary hit a rising half-volley at Evans from 15-yards after Bell's cross from the right.
O'Leary saw another effort fly wide from 23 yards in the 66th minute, before Spring snatched at a decent opening five minutes later, blasting badly wide from four yards at the far post after Drew Talbot had touched on a Bell cross.