The funeral was not attended by Babic's wife and children. A religious service was conducted by several priests from local churches.
The body of the former Croatian Serb rebel leader arrived in Belgrade aboard a flight from Amsterdam on Monday afternoon.
Hague tribunal spokeswoman Aleksandra Milenov told the news agency Tanjug on March 16 that Babic's family had requested privacy regarding the takeover of his remains and the funeral.
The 50-year-old Babic was sentenced to 13 years' imprisonment after in January 2004 he pleaded guilty to charges of war crimes in Croatia. In early March this year he testified in the trial of another Croatian Serb rebel leader, Milan Martic.