The home side had the better chances in a scrappy first half and almost went ahead after 10 minutes but for a tremendous double save from Luton goalkeeper Marlon Beresford.
New-boy Colin Cameron rolled a free-kick into the path of Ben May who hit a fierce low drive that Beresford parried.
Carl Asaba pounced on the rebound but the Luton stopper was there to save at the Millwall striker's feet.
The home side finally broke the deadlock midway through the half through top-scorer May.
The 21-year-old collected a cross from the right wing and shielded the ball well before turning and drilling the ball low and hard past Beresford from 12 yards.
Luton boss Mike Newell was sure to have had some harsh words with his side during the break as they failed to mount any serious attacks throughout the first period.
Sure enough his side were back on level term straight after the break through defender Chris Coyne.
Steve Howard nodded down a Paul Underwood free-kick to Coyne on the edge of the six-yard box and the young defender fired the ball into the roof of the net with a powerful left-foot volley.
The goal fired the visitors into action as they went in search of all three points.
Only a string of excellent save from Millwall Keeper Andy Marshall to deny Carlos Edwards and then Ahmet Brkovic kept his side in the game.
The home side had to cling on as Luton went in search of the win, but it was the Lions who had the last laugh when Williams was fed by Asaba and flicked the ball over the head of the advancing Beresford in injury time.