The 45-year-old Pandurevic is accused of the July 1995 genocide against Muslims in Srebrenica, when Serb troops seized the UN-protected enclave in eastern Bosnia, killing more than 7,000 men of military age.
The indictment charges him with eight counts of genocide, complicity in genocide, executions, persecution and deportation as crimes against humanity and violations of the laws and customs of war.
After Ljubisa Beara and Drago Nikolic, Pandurevic is the third of the so-called Srebrenica Five to surrender. Ljubomir Borovcanin and Vujadin Popovic are still at large.
In the summer of 1995 Pandurevic was commander of the Republika Srpska Army Zvornik Brigade whose members, according to the indictment, between 12 and 19 July deported Muslim women and children to Kladanj, while detaining more than 7,000 men on a number of locations before killing and burying them in an organised and systematic fashion.
Zvornik Brigade troops tried to cover up the crime by digging the corpses from mass graves, transferring them to different locations and reburying them, according to the indictment.
Last year the Hague tribunal sentenced general Radislav Krstic, commander of the Drina Corps, which included the Zvornik Brigade, to 35 years in jail for complicity in the Srebrenica genocide.
The verdict established that Serbs had committed genocide in Srebrenica, the gravest crime under international humanitarian law.