Jabo Ibehre's strike in the 26th minute was enough to see off a Hatters side lacking any invention.
Ibehre blasted in off the crossbar for his fifth of the season meaning Luton have taken just one point out of a possible 21 available under new boss Mick Harford.
The visitors started the better with skipper Stephen Purches hitting a 20-yard shot wide in the eighth minute and Luton goalkeeper Dean Brill denying Ibehre a minute later.
The Hatters' frustrations were evident early on as Lewis Emanuel escaped what appeared to be a head butt aimed at Jason Demetriou on the touchline in the 15th minute.
Demetriou was bizarrely booked for his part in the incident but got his revenge ten minutes later as he was involved in Orient's opener.
A lovely move down the left flank ended with Demetriou back-heeling for Paul Terry to cross.
The midfielder's centre was mis-kicked by Sol Davis straight into the path of Ibehre, who fired in off the crossbar from eight yards.
The half ended with ex-Hatter Adam Boyd testing Brill with a 15-yard shot on the turn after Terry's pass three minutes before the break.
The visitors stayed in the ascendancy after the interval with Brill saving Demetriou's 20-yarder in the 53rd minute, before Steve Robinson cleared Ibehre's header off the line eight minutes later.
Luton registered their first shot on target in the 65th minute when Calvin Andrew fired at Stuart Nelson from 25 yards.
Substitute Paul Furlong went close with a 78th minute header saved by Nelson's knee after Dean Morgan's cross, but Orient held on for the points.