Abdallah Banda Abakaer Nourain and Saleh Mohammed Jerbo Jamus surrendered to the ICC on Wednesday after being secretly indicted last year.
Twelve African Union peacekeepers died in the 2007 attack in Haskanita.
Earlier this year, charges against another rebel leader to do with the same incident were dropped.
ICC judges ruled prosecutors could not prove that Bahr Idriss Abu Garda, who also gave himself up voluntarily, had planned the attack on the Haskanita AU camp in September 2007.
The two are due to face charges of:
- Murder
- Intentionally directing attacks against peacekeeping personnel
- Stealing property
“It is alleged that the attackers, numbering approximately 1,000, were armed with anti-aircraft guns, artillery guns and rocket-propelled grenade launchers,” said an ICC statement.
In January 2008, the UN took joint control of the peacekeeping force in Darfur with increased numbers and a stronger mandate.
Last year, Sudan’s President Omar al-Bashir was indicted on war crimes, which were the first issued by the ICC against a sitting president.
He strongly denies the charges – and his government says figures of those killed in the Darfur conflict have been massively exaggerated.
According to the UN, an estimated 300,000 people have been killed in Darfur and more than 2.6 million displaced since ethnic rebels took up arms in 2003.
A government minister and pro-government militia leader have also been indicted for alleged war crimes in Darfur.
The ICC wants the UN Security Council to press Sudan to hand them over.