Skenderbeu have been removed from Champions League qualifying and replaced by Partizani following a decision from the Court of Arbitration for Sport (CAS).
UEFA confirmed CAS had upheld a decision to declare the Albanian champions ineligible for any of its club competitions amid allegations of match-fixing.
Fellow Albanian outfit Partizani - who had already played the first leg of a Europa League qualifying match against Slovan Bratislava - will now meet Ferencvaros in the second qualifying round of the Champions League.
Slovan will progress automatically to the next round of the continent's secondary competition.
Skenderbeu won a sixth successive Superliga crown last season and featured in the Europa League group stages after being eliminated from the Champions League play-offs.