Wydad president Said Naciri said an "amicable" agreement was reached but did not specify the reasons for Manojlovic's departure.
The 57-year-old Serb took over from Faouzi Benzarti in July, after Wydad finished runners-up to Esperance in a highly controversial CAF Champions League final.
Tunisian club Esperance were awarded the title after Wydad stormed off the field in the second leg after an equaliser was disallowed.
Wydad are second in Group C behind Mamelodi Sundowns in this season's competition with six points from four matches following Saturday's 2-2 draw away to Petro Luanda of Angola.