Gotabaya is the brother of former President Mahinda Rajapksa and served as defence secretary during the end of LTTE war.
In a message, he called for a new journey for Sri Lanka adding that all Sri Lankans are part of this journey.
His main rival Sajith Premadasa has conceded defeat and congratulated Rajapaksa on his victory.
Premadasa has also resigned from his post of deputy leader of United National party under Prime Minister Ranil Wickremsinghe.
Rajapaksa has got overwhelming support in majority-dominated areas of south and is expected to get over 52 percent of overall votes.
Premadasa has received wide support from minority areas in north and east.
The counting of votes is continuing and final results are expected by evening.
The trend shows sharp polarization along community lines, unprecedented in Sri Lankan history.
The cabinet is scheduled to meet this evening to discuss the latest political situation.