The accused, Ramgopal Patel, and the witch doctor, Rajesh Yadav, 19, were arrested on Monday, two days after the incident took place in Amera village under the Palari police station limits, a police official told PTI.
He said the body of the 13-year-old boy lying in a pool of blood was found at his residence in the village on November 25, following which police launched a probe.
"During interrogation, Ramgopal Patel confessed to having killed the boy after the baiga or the witch doctor asked him to offer his son in sacrifice to get rid of evil spirits," the official said.
He said Patel allegedly strangulated his son to death before "cutting his genitals and slitting parts of his head".
According to preliminary information, Yadav told Patel that he was possessed by some evil spirits and that "sacrificing his own son was the only solution to get rid of them".
Police booked Patel under IPC sections related to murder and causing disappearance of evidence, and Yadav on the charge of criminal conspiracy, the official said, adding that further probe was on.