Neiphrezo Keditsu, the NPF candidate retained the Northern Angami-II assembly constituency, held by former chief minister Neiphiu Rio, who vacated the seat after being elected to the Lok Sabha.
Rio represented the Northern Angami-II assembly constituency for five consecutive terms and was the chief minister for three terms.
"Neiphrezo Keditsu defeated BJP candidate Visasolie Lhoungu by 3,045 votes," W. Honje Konyak, Kohima returning officer, told IANS.
Keditsu polled 9,909 votes while his rival candidate Lhoungu secured 6,864 votes.
The BJP, which is supporting the Democratic Alliance of Nagaland (DAN) government headed by T.R. Zeilang, has only one member in the 60-member Nagaland assembly.
Conceding the defeat, BJP's Nagaland president M. Chuba said the party accepted the people's mandate.
"We have lost the by-election, but the party has morally won as the party candidate has managed to get more votes than expected in a constituency which was represented by Rio," Chuba told IANS.
Chuba said that the Bharatiya Janata Party (BJP) will continue to support the NPF-led DAN coalition government in the state.
With Monday's victory, the ruling NPF has increased its strength to 38 in the 60-member assembly, while the opposition Congress has eight legislators.