Irrfan was chosen for his intense portrayal of the steeplechase player Paan Singh Tomar. A seven-time national champion in the '50s and '60s, Tomar, who served in the Indian army, turned a bandit after a land fued in his family. He was killed in 1981.
Gokhale, who has acted in many Hindi films as well, was honoured for his poignant depiction of a man struggling to save his dying wife in Marathi film 'Anumati'.
A beaming Irrfan, 46, dedicated his award to the athlete and his family.
"I am happy that Paan Singh Tomar, who was unknown, became a household name through this film. I share this award with his family. I hope that the film helps people realise that talent should not go to waste," Irrfan told PTI.
Bollywood shared the spotlight with Malayalam and Marathi films with the jury recognising wide variety of movies from different regional cinema industries. Though not in the main categories, Malayalam films bagged 13 awards to emerge at the top.