Alpesh Thakor, who quit the Congress to join BJP last month, was poised to lose his seat while his aide Dhavalsinh Zala was defeated from his constituency.
Turncoats Alpesh Thakor was set to lose the Radhanpur Assembly bypoll in Gujarat, while Zala lost the Bayad seat. Thakor had won the Radhanpur seat on a Congress ticket in 2017.
Earlier in the day, the Congress was leading on four seats while the BJP was ahead on two seats. The BJP had held four of the seats and the Congress two.
The Amraiwadi seat, which earlier in the day saw the Congress consistently ahead, witnessed the BJP making gains after the 17th round. BJP's Ajmalji Thakor won the Kheralu seat, defeating Congress' Thakor Babuji Ujamji by 29,091 votes.
"The credit for my victory goes to party workers," Thakor said after his victory on Kheralu. The Gujarat Congress chief Amit Chavda attacked the BJP, saying the ruling party "has failed on all fronts".
Prominent Congress leader Rajeev Satav thanked voters of Gujarat for their support. "Congress has won three out of six assembly seats," he said. He termed the win significant as Gujarat was the home state of Prime Minister Narendra Modi and Home Minister Amit Shah.
In the 2017 state elections, the Congress under Rahul Gandhi had given the BJP a tough fight, winning around 70 seats, to the BJP's around 100 seats.
"We accept decision of people," said Jitu Vaghani, state BJP chief, after the results.
In Tharad seat, the Congress' Rajput Gulabsinh Pirabhai, won defeating BJP's Patel Jivrajbhai Jagatbhai, with a margin of 6,372 votes.
In Bayad, Congress candidate Patel Jasubhai Shivabhai defeated Dhavalsinh Zala of BJP by 743 votes.
In Amraiwadi, BJP's Jagdish Ishwarbhai Patel was ahead of his Congress rival Patel Dharmendra Shantilal by over 5,000 votes. In Lunawada, the BJP's Jigneshkumar Sevak was ahead of the Congress' Gulabsinh Chauhan by over 13,000 votes.
Deputy Chief Minister Nitin Patel thanked the people of Kheralu seat area for electing BJP candidate Ajmalji Thakor. Nitin Patel was appointed party incharge for the seat located in Mahesana district, which he represents.
Gujarat BJP spokesperson Bharat Pandya said the party had also won two ward seats in Vadodara and Junagadh municipal corporation by-polls.
"We had 100 per cent result in 2014 and 2019. It is not necessary that every time we win 100 per cent seats only. After all, people are supreme. We had 3 seats, and we retained the number. We also increased our lead in Radhanpur and Bayad seats. We analyse result of each seat, whether we win or lose," he said.
"Out of 15 candidates fielded by BJP in municipality by-polls, 13 are victorious," he added.
( With inputs from IANS )