Dhananjay Munde defeated independent candidate Prithviraj Sambhaji Kakde who was backed by BJP.
The bypoll was held to fill the vacancy caused by Munde junior's resignation as BJP MLC elected by members of the Legislative Assembly.
While Dhananjay polled 165 votes, Kakde could secure 106 votes, 59 less than the NCP candidate.
"Kakde got 17 votes more than expected. This is a befitting reply to the politics of NCP leader Ajit Pawar," state BJP president Devendra Fadnavis said, reacting to the result.
In the normal case, his term of office would have ended on July 7, 2016.
On the last day of filing nomination papers, BJP had fielded its former Aurangabad city unit president Basavraj Mangrule and former Samajwadi Party worker, Shriprakash Shukla, as its official candidates.
However, the two withdrew from the fray and were present at a media briefing by Gopinath Munde later where he said BJP had decided to back the candidature of Prithviraj Kakde, who filed his nomination papers as an independent candidate.
Congress has 82 MLAs, NCP has 62, BJP 46, Shiv Sena 44, MNS 12 while small parties and independents make up 39 members.
