Colchester failed to clear in the first half and Mark Cullen capitalised on that by smashing the Football League newcomers into the lead.
The visitors were soon level after an unfortunate own-goal from Luton right-back Paul Connolly and the U's were soon ahead as Jabo Ibehre tucked home after he was set through by former West Ham man Freddie Sears.
Luke Guttridge, making his first Hatters appearance since he was stretchered off in March, coolly finished after good work from Cullen out wide. The equaliser gave the home side momentum and they looked more likely to score, but Colchester held on to share the spoils.
Luton will face more League One opposition in the shape of Peterborough on Saturday, seven days before their season kicks off at Carlisle.