Bhattacharya, who had lost the Lok Sabha election from the state earlier this year, was trailing Bishwas by over 17,000 votes at the half-way stage but made it up by winning by a margin of over 18,000 votes in the urban pockets.
The seat fell vacant after the death of CPI(M)'s Narayan Mukherjee who won there in the 2011 assembly elections.
The battle for the Basirhat South constituency was a prestigious one as 17 TMC ministers of the state had camped there ahead of the polling to tackle the BJP factor. But yet the ruling party could not stop the BJP from winning its first seat in the assembly. Reacting to the victory, Bhattacharya said it is a victory of the people of Bengal.
In 1999, BJP's Badal Bhattacharya had won a bypoll from Ashoknagar but then the BJP was in alliance with the Trinamool Congress.
In another bypoll, TMC's Nayana Bandyopadhyay, wife of party's PM Sudip Bandyopadhyay, won from Chowringee seat.