Luton almost took the lead early on when stand-in captain Jonathan Smith cannoned the post from 20 yards, but it was Cambridge who made their early pressure count when keeper Mark Tyler brought down Ryan Donaldson in the penalty box to concede a spot kick.
Tyler managed to save Robbie Simpson's effort, but the striker hammered in the rebound to give the hosts the lead.
The Hatters pressed for an immediate equaliser and they almost found one when a corner was headed across goal for Jim Stevenson, but he put the ball over the bar from the edge of the box.
Luton continued to pressurise Cambridge in the early stages of the second half, and they went close to equalising when Michael Harriman's cross was put wide by Andy Drury from just two yards.
That miss seemed to give Cambridge confidence and, after he hit the crossbar from a Luke Chadwick pass, Donaldson doubled their lead when he slipped past a defender and slotted home inside the box.
Luton managed to respond immediately as Drury's curling cross found Harriman at the back post to put them back in the game, and they then almost equalised through Greg Taylor but he couldn't get his effort on target from a Harriman cross, and Cambridge hung on to claim the win.