Jonny Gorman's 85th-minute free-kick was turned into his own net by Andreas Christofides to end a run of five straight defeats in Group Nine.
It was the home side's first shot on target of a largely lifeless encounter and they may have even had a second when Gorman drew a good save from Giorgos Loizou in the final stages.
Jim Magilton took charge with Stephen Robinson away with the Under-17s and had reason to be content after his side came back into the dressing-room level.
Ryan Brobbell had an early effort blocked and they were hardly troubled at the other end, with only a wayward effort from Cyprus captain Pieros Sotiriou causing any alarm.
Northern Ireland goalkeeper Conor Brennan kept out the first shot on target on 62 minutes when Kostakis Artymatas finally made him work.
Cyprus, a place above Northern Ireland in the group with six points, threatened through Sotiriou and Nikos Efthimiou but a draw seemed the most likely result until Gorman's late intervention.
His free-kick was turned in by Christofides to give Northern Ireland just their second goal of the campaign and the three points.
Gorman almost got his name on the scoresheet soon after, but Loizou made a good save.