Congress, which shares power with NCP at the state level, went alone in elections to the 81-member Nanded Municipal Corporation, held yesterday.
While NCP secured 10 seats, Shiv Sena got 14 and BJP won on 2 seats.
Reacting to the victory, former Maharashtra Chief Minister Ashok Chavan who led the party in the polls, said the win was possible due to "teamwork" among Congress workers.
"I will give all credit to party workers. The victory was a result of teamwork and stress on developmental issues and inspiration of our leader Sonia Gandhi," Mr Chavan said, terming the results a victory of "people's power"
NCP leader Pratap Chikhlikar, a staunch rival of Ashok Chavan in Nanded, alleged that Congress "used money power" to win the elections.
Nanded is the home constituency of Ashok Chavan and the polls were considered crucial for his political future.
Mr Chavan has been looking at consolidating his position in Nanded and the larger Marathwada region to fill the leadership vacuum created in Congress following Vilasrao Deshkmukh's demise.
Chief Minister Prithviraj Chavan, Industries Minister Narayan Rane and other senior Congress leaders had campaigned for the Congress.
NCP leader Ajit Pawar had also held a rally during the campaign.
The Sena-BJP-RPI alliance, which had fielded candidates in 72 seats, won 16 out of them.
Its campaign witnessed a road show by Sena executive president Udhhav Thackeray's son Aditya. MNS contested 42 seats but party chief Raj Thackeray did not campaign.
The Hyderabad-based All India Majlis-E-Ittehadul Muslimeen fielded 25 candidates and won 11.
Three independents also won in the elections.
The Shiv Sena had offered a pre-poll alliance to the MNS which spurned the offer.
Earlier, the Shiv Sena and the MNS had reached post-election understandings in places like Ambernath, Thane and Kalyan-Dombivali.