A goal just before half time from Josh Doherty gave the hosts the lead but goals from Enis Bardi and Kire Markovski completed the comeback for the Macedonians.
Both sides had a fair share of the possession in the first half but it was Macedonia who threatened to take the lead.
10 minutes had gone when David Babunski for the visitors had the first shot on goal but Northern Ireland keeper Conor Brennan matched the striker’s effort to push it round the post.
Brennan would be kept busy throughout the half and after 24 minutes a freekick from Bardi was hit hard but once again saved by the Northern Irish stopper.
Only two minutes had passed when the best chance of the half for the visitors was wasted. Marjan Radeski’s shot was flicked on by Visar Musliu inside the six yard box but his effort went over the bar.
Musliu was back in the action again after 36 minutes as he could only send his header from a corner across Brennan’s goal.
Macedonia kept coming and just a minute later they came even closer to taking the lead as Daniel Avramovski’s header hit the base of the post and went behind for a goal kick.
However, it was Northern Ireland that took the lead on the stroke of half time. A corner from Darren McKnight was met by Liam Donnelly whose header was then directed towards goal by Doherty to put the hosts 1-0 up at half time.
However the lead lasted 60 seconds into the second half as half time substitute Viktor Angelov setup Enis Bardi to curl round Brennan and into the bottom corner to equalise.
Northern Ireland’s evening then began to go from bad to worse as James Singleton came out on the wrong side of a 50/50 challenge and had to leave the pitch on a stretcher.
With just ten minutes of normal time remaining, the game sparked into life in a crazy five minute period. First, the visitors hit the post again after an effort from Babunski which cannoned off the post and was scrambled away.
It was then Northern Ireland’s turn on 83 minutes as Mikhail Kennedy was played through but he was unable to take the opportunity as he could only hit the side netting.
That miss was punished just two minutes later as Macedonia completed their comeback. It was the substitute Angelov once again being the provider but this time for Markovski to slot home under no pressure inside the box for a 2-1 lead.
That’s how it finished at Mourneview Park with Northern Ireland still on one point after three games in Group C. Their next fixture takes them to France on November 12.
Northern Ireland: Brennan, Dummigan, Sharpe, Donnelly ©, Doherty, McKnight, Whyte (86), Singleton (70), Kennedy (88), Camps, Duffy. Subs: Mitchell, Conlan, Cooper, McDonagh, Maloney (86), McCarten (70), McDaid (88)
Macedonia: Aleksovski, Musliu, Zajkov ©, Bardi, Nikolov, Radeski (88), Babunski (90+3), Avramovski (45), Markoski, Demiri, Murati. Subs: Siskovski, Ristovski, Amanovic, Kostadinov (88), Angelov (45), Imeri, Mustafov (93)