Despite losing 4-1 in Korçë the Crues do have that away goal to potentially use as a springboard to recover the tie next Tuesday night at Seaview.
Skënderbeu moved in front after a quarter-of-an-hour through Bakary Nimaga before Hamdi Salihi doubled their advantage on 34 minutes.
However, barely three minutes into the second half, Owens grabbed what could prove to be a crucial away goal for Stephen Baxter's side after nodding a superb long range pass from Billy Joe Burns beyond past Albanian international 'keeper Orges Shehi.
The hosts restored their two-goal cushion on 76 minutes courtesy of a Bernard Berisha finish with Salihi adding a fourth six minutes from time.