A National Transitional Council (NTC) official said the bodies were buried at dawn in an unknown location.
The burial news comes after days of uncertainty among the new leadership about what to do with the bodies. The Misratan military brigades who captured and killed Gaddafi were reluctant to hand over their trophy corpse.
Gaddafi’s family wanted him buried outside the former leader’s hometown of Sirte. Nut it is unclear if their wishes were granted.
The ceremony took place early on Tuesday, with just a few relatives and officials in attendance and Islamic prayers were read.
Libya’s Minister for Information Mahmoud Shammam said the NTC was following a fatwa, or religious ruling.
“It says that his body should not be buried in Muslim cemeteries and should not be buried in a known place to avoid any sedition,” Mr Shammam said.
An NTC official had earlier told Reuters news agency that Col Gaddafi would be buried in a “simple” ceremony with “sheikhs attending” on Tuesday.
“It will be an unknown location in the open desert,” he said, adding that a burial was needed because decomposition of the body had reached the point where the “corpse cannot last any longer”.
Gaddafi, Mutassim and former Defence Minister Abu Bakr Younis Jabr were killed on Thursday following the fall of Sirte, the last major pro-Gaddafi bastion.
Witnesses said the bodies had been removed late on Monday from the meat storage warehouse in Misrata where they had been on display.
Islamic tradition dictates a burial should happen within a day of the death.
But the NTC leadership was concerned that any public grave could become a shrine for Gaddafi loyalists or a target of hatred for those who opposed his regime.