The last rites were performed at 11.30 a.m. at the Versova crematorium close to his residence in the presence of Raza Murad, Tabassum and family members, a family member said.
His niece Kajol, music composer Bappi Lahiri and veteran actor Tabassum were present at his residence before the body was taken to the crematorium.
The actor, who stepped into filmdom in 1960 with "Love In Simla", died at the Lilavati Hospital here Friday morning. He was 73.
He was admitted to the hospital March 5 and had been on ventilator since then.
He is survived by his wife Neelam Mukherjee, two sons and a daughter.
Joy Mukherjee came from a film family. His father Sashadhar Mukherjee was married to legendary actor Ashok Kumar's sister Sati Devi and was the co-founder of Filmalaya Studios.
Joy Mukherjee featured in films like "Love In Tokyo", "Ziddi", "Phir Wohi Dil Laya Hoon" and "Ek Musafir Ek Hasina".