Independent candidate Utpal Parrikar, the son of Goa's former chief minister Manohar Parrikar, lost to BJP's Atanasio Monserratte from the Panaji Assembly seat on Thursday.
After the end of last round of counting, Monserratte won by 674 votes, an election official said.
"I gave a good fight," Utpal Parrikar, who bagged 5,857 votes, said while leaving the counting station.
Monserratte polled 6,531 votes, while Congress candidate Elvis Gomes got 3,062 votes. After the BJP refused ticket to Utpal Parrikar, he contested the election as an independent.
Monserratte said the BJP cadres in the state capital Panaji did not accept Utpal Parrikar in the party.
"I am disappointed as far as results are concerned. BJP cadre didn't work for me but for the Opposition candidate. I fought BJP and Congress. It's due to the support of a few workers and supporters that we managed to retain the seat.
"I feel BJP cadre hasn't accepted me into the party. I look at it in that way. If he (Utpal Parrikar) can get so many votes, it's just because the cadre shifted their votes to him. BJP leadership here didn't manage to do damage control," Monserratte said.