Muzammil (32), a resident of Bihar, went missing since November 27, and on the complaint made by his brother Nadeem a probe was started into the matter, they said.
Two accused Sandeep Singh and Santosh, during interrogation, told police that they had buried Muzammil's body near the river bank at Hanumanti.
The body was exhumed and sent for post mortem, Inspector Subhash Dhyani said.
The motive behind the crime was yet to be ascertained, police said.