Maintaining his lead right from the initial rounds of counting Rajendra Gavit led BJP to its first victory by a margin of 25,723 votes.
BJP secured 214,030 votes while Shiv Sena got 188,307 votes.
By-polls were held on two seats Palghar and Bhandara-Gondiya in Maharashtra.
At the end of eight rounds of counting in Palghar, Gavit had maintained his lead by securing 91,795 votes while Shiv Sena's Shrinivas Wanaga got 73,387 votes.
After the first round of counting, Gavit was leading by 146 votes.
In Maharashtra's Palghar, it was said to be a neck-to-neck fight between BJP and Shiv Sena, but in the middle of the course Bahujan Vikas Aghadi emerged ahead of Shiv Sena, making it a BJP Vs BVA fight.
The by-election in Palghar was necessitated due to the death of sitting BJP MP Chintaman Wanaga.
The results of the two Lok Sabha by-polls in Maharashtra are important for all four major political parties - BJP, Shiv Sena, Congress and NCP - as the outcome is likely to have a bearing on their future course of action.
The polling, held on Monday, was marred by allegations of malfunctioning in the electronic voting.
Re-polling was ordered in Bhandara-Gondiya but not in Palghar.
As many as 25 candidates were in the fray for the two seats - 18 in Bhandara-Gondiya and seven in Palghar.