The apex court bench headed by Justice Kurian Joseph granted Ekbote interim protection from arrest till February 20.
It also sought a response from the Maharashtra government on his plea for anticipatory bail.
On Jan 29, Ekbote's plea was mentioned before the bench, led by Justice Gavai after a sessions court refused to grant him any interim protection from arrest.
Earlier last month, a special court in Pune had rejected a plea for anticipatory bail filed by Ekbote, in regards to the same case.
Two FIRs were registered against Ekbote alleging his role in the violence at Bhima Koregaon at a time when Dalits in huge numbers had gathered in Perne village to mark 200th year of the Battle of Bhima Koregaon.
Ekbote is facing charges for inciting violence, attempt to murder and atrocities against Dalits.
On January 1, the violence left at Bhima Koregaon left one dead and injured several others, including 10 policemen. (ANI)