Dhananjay is the Leader of Opposition in the Maharashtra Legislative Council.
His panel won 14 out of the 18 seats, for which 42 candidates were in the fray.
The Parli APMC was earlier controlled by Pankaja's father, the late BJP stalwart Gopinath Munde for around three decades.
In the elections held in 2010, panel fielded by Pandit Anna Munde, Dhananjay's father and Gopinath Munde's elder brother, emerged winner.
Dhananjay, who was with the BJP, subsequently joined NCP in 2012.
"The BJP tried to use a lot of money power to win these polls," alleged Dhananjay.
"However, we had the strength of people which resulted in our victory," he said.