The last rites were performed at 11.30am 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 Bollywood in 1960 with Love In Simla, died on Friday morning. He was 73.
He was admitted to the hospital on March 5 and had been on ventilator since then.
He is survived by his wife Neelam, two sons and a daughter.
Mukherjee featured in films like Love In Tokyo, Ziddi, Phir Wohi Dil Laya Hoon and Ek Musafir Ek Hasina.