The 56-year-old Serb signed an 18-month deal with Al Ahly, the Ghana Football Association said in a brief statement on Tuesday.
The Ghana Football Association (GFA) said last month Rajevac was close to signing a new contract.
"The GFA has officially been notified by Mr. Milovan Rajevac of his desire to take up a fresh challenge elsewhere," the GFA said.
"He relinquishes his position as head coach of the Black Stars after two years and the GFA would like to place on record our gratitude for his services and wish him all the best in his future career.
"Though we find his departure unfortunate after two years of great strides, we confirm the search for a new coach has begun."
The quietly-spoken Rajevac emerged from coaching anonymity to make a big impact during his two years in charge of the Black Stars.
Ghana qualified in style for the World Cup finals in South Africa and also reached the final of the African Nations Cup in Angola at the start of the year.
The team's charge to the last eight of the World Cup was all the more impressive as they were without midfield talisman, Chelsea's Michael Essien, through injury.
Rajevac's departure means all six coaches in charge of African teams at the World Cup have now left their posts. Algeria's Rabah Saadane resigned earlier this month while the coaches of Cameroon, Ivory Coast, Nigeria and South Africa departed after the tournament.
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