The 91-year-old Padamsee died of natural causes and the last rites were performed at the Centre the same night in the presence of his family, an Isha release said on Tuesday.
Paying tributes to the artist, Sadhguru Jaggi Vasudev, Founder, Isha Foundation said "Akbar Padamsee, a genius of colour and craft, it has been our fortune to have you spend the last part of your life with us at Isha Yoga Centre.
Generations to come shall relish and be inspired by your magic of color."
For the last few years, Padamsee and his wife Bhanu were residents of the Isha Yoga Centre.
After visiting the centre a few times, they decided to move in permanently.
Padamsee refused to fit into any artistic compartment, the release said.
He did not want anyone to label him or his art, the release said.
Though Akbar was best known for his radical paintings, he was also a photographer, sculptor, filmmaker, engraver and lithographer.
But Padamsee was most recognized and decorated for his paintings which have found a place of prominence in eminent galleries in India and around the world.
His brother was the celebrated late filmmaker and adman Alyque Padamsee.
Padamsee was awarded the Padma Bhushan in 2010 and was also awarded Fellowships by the Lalit Kala Akademi and the JD Rockefeller Foundation apart from recognition by several global art bodies.
The family took on the name 'Padamsee' when his grandfather earned the title 'Padmashree' after he distributed the entire grains in his granary to his village in Kutch during a famine, the release said.