The amendment was brought by former party president Rajnath Singh, and seconded by another former president M. Venkaiah Naidu.
Announcing the amendment, party's general secretary J.P. Nadda said it will also enable extending the tenure of district and state presidents of the party.
"Earlier, a president could have only one term of three years at a time. Now a president can have two consecutive terms of three years at one stretch," he said.
Nadda added that the amendment was passed "unanimously" by voice vote. No discussion was held on the amendment.
Asked if Gujarat Chief Minister Narendra Modi or any other member expressed an opinion otherwise, Nadda said "all members act objectively in such issues".
Gadkari, who enjoys the backing of the Rashtriya Swayamsewak Sangh (RSS), became the party president in 2009. His term was to expire in November this year.
The extension is being seen as an effort from the party to reconcile before the 2014 general elections, and be prepared in case of a mid-term poll.
Sources, however, say that not all leaders are happy with Gadkari, but the party president is now being seen making efforts to increase his popularity. Gadkari's decision to let go Modi's old foe Sanjay Joshi is also being seen as a part of efforts to settle differences.
The party also initiated its process for admitting workers to the party and holding elections for the posts in the party.
Uttar Pradesh BJP leader Radha Mohan Singh was selected as the incharge for admitting new members, while Rajya Sabha member Thaawar Chand Gehlot will be incharge of elections.
The two-day national executive meet of BJP ends Friday.