Macedonian champions Vardar will face Turkey's Fenerbahce, while league runners-up Shkendija goes against Italian giants Milan in the UEFA Europa League play-offs, decided a draw in Nyon on Friday.
The ties are played on 17 and 24 August.
A Macedonian club has never qualified for a group stage in a UEFA-run competition. Shkendija and Rabotnicki came close in the Europa League in recent years but failed in the play-offs.