While Dr Neiphrezo Keditsu of NPF polled 9,909 votes, BJP candidate Visasolie Lhoungu received 6,864 votes, District Returning Officer and DC Kohima, W Honje Konyak said.
Both BJP and NPF are allies in the NPF-led Democratic Alliance of Nagaland (DAN) government.
The seat had been previously held for five continuous terms by three-times Chief Minister Neiphiu Rio from 1989 till May 2014.
The bypoll was necessitated following Neiphiu Rio's win in the Lok Sabha election in May this year.