The coffin of Andrei Karlov, draped in the Russian flag, was loaded onto the plane by an honour guard of six Turkish soldiers following a ceremony on the tarmac of Esenboga airport, an AFP photographer said.
The ceremony was attended by his widow, Turkish Interior Minister Suleyman Soylu, Deputy Prime Minister Tugrul Turkes and top Ankara-based diplomats.
In a highly unusual scene at an airport in mainly Muslim Turkey, a Russian Orthodox priest said prayers and swung incense over the coffin.
Before the coffin was taken away to the plane, his widow stepped forward and kissed the coffin in a tearful final farewell.
The plane is due to arrive in Moscow later in the evening.
Karlov was shot nine times in the back by Turkish policeman Mevlut Mert Altintas, 22, in a brazen attack as he opened an exhibition of Russian photography yesterday.