New Northern Ireland Under-21 coach Stephen Robinson was unable to reverse the team's poor Euro 2013 qualifying record as they lost his first match in charge to a late penalty.
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Robinson, who inherited the side from Steve Beaglehole, saw his side concede two penalties - the second converted by Yani Urdinov for an 83rd-minute winner.
There was also a late red card for Newcastle's Shane Ferguson as the young Northern Ireland side lost for the fourth time in six qualifiers.
This match was rearranged after freezing conditions in Kumanovo caused its postponement in February, allowing Robinson to call on a handful of players with senior caps - including Ferguson, Ryan McGivern, Lee Hodson and Oliver Norwood.
But their presence did not lift the side in a low-key first half that saw virtually no meaningful chances for either side.
Norwood looked Northern Ireland's best outlet, shooting wide both sides of half-time, but a Seanan Clucas foul allowed Macedonia the chance to go ahead through a 53rd-minute penalty which Ilija Nestorovski blazed over.
A goalless draw looked the most likely outcome until the hosts earned a second spot-kick, with Urdinov converting.
That left Robinson's side just seven minutes to find an equaliser but instead their night got worse, with Ferguson red-carded for an off-the-ball incident.
FYR Macedonia U21 Gacevski, Ristovski, Ristevski, Urdinov, Bogdanovic, Tairi, Fazli (Altiparmakovski 71), Nestorovski (Babunski 57), Hasani, Brdarovski (Timov 77), Spirovski.
Subs Not Used: Dimitrievski, Husmani, Askovski, Siljanovski.
Booked: Urdinov, Spirovski, Ristevski, Brdarovski.
Goals: Urdinov 83 pen.
N Ireland U21 Devlin, Hodson, McGivern, Thompson, Conor McLaughlin, Clucas, Ryan McLaughlin (Lavery 77), Norwood, Grigg, Lund (McClure 86), Ferguson.
Subs Not Used: Deane, Watson, McCartan, Morgan, McKeown.
Sent Off: Ferguson (88).
Booked: Ryan McLaughlin, Clucas, Norwood, Devlin.
Ref: Davit Kharitonashvili (Georgia).