Wydad "is considered to have lost the game", African football's governing body said in a statement.
The Moroccan side walked off an hour into the return leg in Tunis after a VAR malfunction meant a disallowed equaliser could not be reviewed.
Wydad were issued a fine for abandoning the match and for the use of flares by supporters.
Esperance, who retained their title won in 2018, were fined and were ordered to play two matches behind closed doors -- a punishment suspended for 12 months.
CAF had called for the second leg to be replayed at a neutral venue, but that decision was overruled last week by the Court of Arbitration for Sport (CAS).
"Justice has been done," Esperance secretary general Farouk Kattou told AFP. "It's a fully deserved title. It's taken two months but finally we have it."