Chief Minister Laxmikant Parsekar lost the Mandrem assembly seat by a margin of nearly 5,000 votes to Congress rival Dayanand Sopte.
While Parsekar exited the counting Centre in Panaji without speaking to reporters, Dayanand Sopte dedicated the victory to his party workers and said that the people were unhappy with Parsekar's work.
"The margin of nearly 5,000 votes shows that the people were unhappy with the CM's work," Sopte said.
Meanwhile, Goa Deputy Chief Minister Francis D'Souza retained the Mapusa assembly seat in North Goa, defeating his nearest Maharashtrawadi Gomantak Party rival Vinod Phadke by 6,828 votes.
This is the sixth consecutive time that D'Souza has won the Mapusa assembly seat and he is the seniormost elected BJP legislator in the state.
Counting of votes polled in the February 4 Goa assembly election got under way at 8 am amid tight security. For the 40 seats in the state, the BJP had fielded candidates in 36 seats, the AAP in 39, Congress in 37 and the Maharashtrawadi Gomantak Party in 25.
The tenure of Goa Assembly is due to end on March 18.