The body of the boy was recovered from a well in Ablod village in Garbada taluka last week, police said on Thursday.
Dashrat Bhilwa, of Ukardi village, was arrested on Thursday morning on the charge of throwing his son Devraj into the well on December 31, police said.
When the body was found, a case of accidental death was registered. But the probe revealed that it was a murder.
Bhilwa,had two wives, as is common in his community; Devraj was born of the second marriage.
Bhilwa divorced his second wife some time ago under the tribal customs, but agreed to keep Devraj with him. However, his first wife allegedly did not want the boy, and asked her husband to send him to his mother.
When Bhilwa went to his divorced wife, she refused to take the son back. Following this, he allegedly threw the boy into the well, causing his death.