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.
Argentine Miguel Gamondi, a former assistant at Esperance and head coach at USM Alger, will replace Manojlovic, the club added.
Gamondi, 53, was sacked by another Moroccan side, Hassania Agadir, in November.
Wydad are second in Group C behind Mamelodi Sundowns in this season’s Champions League with six points from four games following Saturday’s 2-2 draw away to Petro Luanda of Angola.
