He had been in and out of hospital several times since being toppled by a pro-democracy uprising during the 1997-1998 Asian financial crisis for heart problems and internal bleeding.
Opinion on his rule remains divided in Indonesia.
Historians say up to 800,000 alleged communist sympathisers were killed during Suharto's rise to power from 1965 to 1968. His troops killed another 300,000 in military operations against independence movements in Papua, Aceh and East Timor.
Suharto's poor health has kept him from facing trial, and no one has been punished for the killings.
Juan Felix Tampubolon, a former lawyer for Suharto, said it was doubtful that criminal proceedings will be launched against the former leader.
He told Al Jazeera: "According to Indonesian law, once a person has died, there would be no more legal action put forward against the person."