The bodies of the men, who were killed in a US raid in Mosul in July, had been flown to Tikrit from Baghdad after being released by US forces.
Saddam's grandson Mustapha, 14, who also died in the raid, was also buried.
The ceremony was "quiet and uneventful" said a US military official, and no violence was reported.
A BBC reporter said tiny groups of Saddam Hussein loyalists have come to pray at the graves.
She said while most Iraqis despised the two brothers, many people felt they still deserved a Muslim burial.