Coach Roy Millar was hampered by a round of fixtures in the Carnegie Irish Premier Division being played on Tuesday night, and he chose to give some of his fringe players a run-out.
The visitors took the lead after 32 minutes through Ciprian Deac, and captain Claudiu Keseru profited from some sloppy Northern Ireland play to put Romania two up on the stroke of half-time.
Millar's side improved in the second half and deserved a goal, which they got when substitute Tommy Stewart tapped in at the far post.
Northern Ireland pushed for an equaliser, and Chris Turner saw a shot well-saved - while a goalmouth scramble also came to nothing.
Keseru came up with a sucker punch 20 minutes from time when he seized on a stray Northern Ireland pass to make it 3-1.
Romania are battling with Wales to qualify from Group 10 for the European Under-21 Championship, while Northern Ireland face a crunch match against Germany in September.