However, Henrique netted a 90th-minute winner to give the French side all three points in Group F.
Sane opened the scoring for the French side when he evaded his marker from a short corner to finish at the near post.
However, with half time looming, the Cypriot side got themselves back in it when Goncalves took advantage of a lapse in concentration from the home side to level things up.
Efstathios Aloneftis hit the post for APOEL on the hour mark when he fired a low shot in from long-range.
With the game seemingly petering out for a draw, Henrique popped up with a header past Urko Pardo to give his side the win.