The attack was allegedly carried out by fighters from the Sudanese Liberation Army-Unity under the command of Jerbo, and splinter forces of the Justice and Equality Movement led by Banda.
"It is alleged that the attackers, numbering approximately 1,000, were armed with anti-aircraft guns, artillery guns and rocket propelled grenade launchers," the court statement said.
The men allegedly destroyed Amis infrastructure and stole items like refrigerators, computers, mobile phones, vehicles, fuel, ammunition and money.
A pre-trial chamber had found reasonable grounds to believe that Banda and Jerbo were criminally responsible for murder, an intentional attack on peacekeepers, and pillaging, the statement said.
"This is the culmination of months of efforts to secure the co-operation of Mr Banda and Mr Jerbo," Luis Moreno-Ocampo, the ICC prosecutor, said in a separate statement.
"The rebel commanders will now face justice," said Moreno-Ocampo.
"Their attack on the camp caused the death of 12 people and worsened the plight of the thousands of civilians they came to help by leaving them without protection."
A further hearing will be held "within a reasonable time" to confirm the charges against them, a requirement before the case can go to trial.
ICC judges have turned down a prosecution bid to prosecute Bahar Idriss Abu Garda, another rebel leader, over the Haskanita attack, finding insufficient evidence to link him to the killings.
He had also appeared before the ICC voluntarily.
The case is the fourth before the court involving alleged war crimes in Darfur.
Arrest warrants are outstanding for Omar al-Bashir, Sudan's president, Ahmed Haroun, a former government minister, and Ali Kosheib, a militia leader.
Al-Bashir rejects the jurisdiction of the ICC, the world's only independent, permanent court with authority to try genocide, crimes against humanity and war crimes, and has refused to hand over his two allies.