Juraj Piroska opened the scoring for the visitors in the 54th minute, but Nikolce Noveski equalised 11 minutes from time to ensure a share of the spoils.
Both teams headed into the encounter knowing they had no chance of qualifying or even improving on their positions in Group B with Slovakia in fourth and Macedonia in fifth.
There were few opportunities of note in the first half, Slovakian midfielder Vladimir Weiss firing wide when well placed in the 13th minute and Macedonian striker Ivan Trickovski seeing a fierce free-kick parried by visiting goalkeeper Jan Mucha.
The deadlock was broken within nine minutes of the restart, though, FK Senica frontman Piroska lashing a low right-footed shot past Macedonia goalkeeper Martin Bogatinov from close range.
Bogatinov had to be alert four minutes later to keep his side in the match, getting his body in the way of a Marek Hamsik blast and then saving another effort from Weiss in quick succession.
Ivanovski and Muhamed Demiri were off target when well placed for Macedonia, but the warning signs were there for Slovakia and the hosts duly got back on level terms in the 79th minute when Noveski headed home Trickovski's corner.
Slovakia had one final sight of goal in the 89th minute, but Bogatinov was in the right place to deny Lubomir Michalik.