Kovacs double too much for BluesTwo goals from Janos Kovacs inflicted a first defeat of the pre-season campaign on Town.
The Hatters' defender headed home from a corner just past the half hour mark, then sealed the victory for Paul Buckle's side with another header in the closing stages.
Michael Chopra and Luke Hyam both went close for Blues, while Massimo Luongo impressed again in another 90 minutes after joining on a season long loan from Tottenham last week.
Jimmy Bullard brought the first save of note with a volley from the edge of the box that tested Mark Tyler, while at the other end Stuart Fleetwood sent a free-kick wide from 22 yards.
Luton created the better chances in the early exchanges and should have gone ahead on the quarter hour but Andre Gray miskicked in front of goal, Scott Loach then doing well to keep out Scott Rendell's effort after the ball ran loose at the far post.
Chopra brought a save from Tyler with a volley but Luton continued to threaten, Fleetwood seeing a header cleared inside the Town box, then Gray putting the ball in the net but not before the offside flag was raised.
Chopra was inches away with a header from a Bullard free-kick but it was the Hatters who opened the scoring on 36 minutes, Kovacs' header from a corner evading Andy Drury on the line.
Town responded with a shot from Bullard that was beaten out by Tyler, the 'keeper then reacting quickly to save the rebound from Ryan Stevenson.
Tyler was called into action again seconds later, Chopra taking advantage of a Cheick Kourouma cross but the 'keeper blocked his path.
Arran Lee-Barrett replaced Loach in goal as Town made six changes at the break. Aaron Cresswell and Carlos Edwards lining up at full-back, with Hyam, Jay Emmanuel-Thomas and Jason Scotland all joining the action. Jack Ainsley, Joe Whight, Bullard, Kourouma and Chopra made way.
Tyler saved spectacularly from Hyam's volley inside the first two minutes of the second-half, the Academy product then setting up Stevenson who blasted over.
Edwards and Scotland combined down the right to bring a save from Tyler at his near post, while on the other flank, Blues couldn't convert Cresswell's cross.
Tyler was tested again as Town threatened an equaliser, Emmanuel-Thomas' left foot effort beaten out at the near post but Paul Jewell's side needed the intervention of Cresswell on the line to prevent Kovacs adding a second 20 minutes from time.
Nathan Ellington replaced Stevenson as the Town boss shuffled his pack but Luton wrapped up the win at Kenilworth Road with Kovacs left with a free header from a free-kick four minutes from time.