Health Minister Vishwajit Rane won the Valpoi seat with a margin of 10,066 votes.
Parrikar, who won the Panaji seat for the sixth time, polled 9,862 votes beating his nearest rival Congress' Girish Chodankar, who netted 5,059 votes. Anand Shirodkar of the Goa Suraksha Manch came a distant third with 220 votes.
"I was expecting to win," Parrikar told reporters after the victory.
Following the former Defence Minister's victory, Union Home Minister Rajnath Singh tweeted: "Spoke to Goa Chief Minister and congratulated him on his impressive victory..."
Chodankar said he may have lost the polls, but he was touched by the manner in which Panaji voters had interacted with him.
"I may have lost numerically, but residents of Panaji have given me a lot of love," Chodankar told reporters here.
In Valpoi, the winning Bharatiya Janata Party candidate Rane got 16,167 votes, while his rival from the Congress, Roy Naik netted 6,101 votes.
Nearly 75 per cent voting was recorded during the August 23 bypolls in Goa.
The bypoll in Panaji was necessitated after former Defence Minister Parrikar's return to state politics in March as Chief Minister.
Sitting BJP MLA Sidarth Kuncolienkar resigned from the Panaji seat, enabling the four time Chief Minister and five-time Panaji MLA to contest for the state's capital constituency.
In Valpoi, the bypolls were held following the resignation of Rane as a Congress MLA. He subsequently joined the BJP and joined the cabinet as Health Minister.
"I am overwhelmed by the victory and the support by my people," Rane said, alleging that the mine-owning lobby tried its best to defeat him.