It was always going to be a tall order for Stephen Baxter's side, trailing 4-1 from the first leg, but they were given a boost after just 11 minutes when Skënderbeu were reduced to ten men following Renato Arapi's dismissal for an off the ball incident with Billy Joe Burns.
Skenderbeu Korce will now play Moldovan side Milsami Orhei in the penultimate Champions League qualifying round.