Irrfan won the award for his portrayal of an athlete-turned-dacoit, while veteran actor Gokhale won for his role in Marathi film Anumati.
The Tigmanshu Dhulia-directed Paan Singh Tomar was also named the Best Film at the 60th National Film awards announced today.
Based on a real-life story, the film won many awards this season and brought the limelight on 46-year-old Irrfan.
"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 waste. The young generation is very talented and their talent should be recognised," Irrfan told PTI.
Dhulia, says he was expecting a win for Irrfan, with whom he has previously worked in Haasil and the recently released Saheb Biwi Aur Gangster Returns.
"I wasn't expecting a Best Film award but I knew Irrfan would win. I am really happy for him and that his hard work has paid off. There were so many good releases this year and to get a recognition such as a National award means a lot," Dhulia told PTI.
Veteran actor Annu Kapoor won the Best Supporting actor award for his role of a fertility expert in John Abraham produced Vicky Donor.
The 57-year-old dedicated his win to his late mother, saying, "I feel humbled and express my gratitude for the national award which I dedicate to my mother, late Kamal Kapoor."
Vicky Donor won a total of three National Awards including Best Supporting actress to Dolly Ahluwalia and best popular film providing wholesome entertainment.
Director Shoojit Sircar said he wasn't expecting such a grand scale win for the movie and is pleasantly surprised.
"I am really excited. I am also surprised because I did not expect Vicky Donor to win in the Popular film category. I am very happy for John (Abraham, producer) and writer Juhi Chaturvedi. I am also very happy for Anuu Kapoor and Dolly Ahluwalia for winning in the supporting categories," Sircar told PTI.
The film's lead actor Ayushmann Khurrana also expressed his gratitude as his debut movie won three National Awards.
"The National Award is the biggest honour a film or an artiste can get in our country. It's extremely overwhelming and I'm proud to be a part of this project which has a rare combo of quirk and credibility," he tweeted.
For his stellar performances in films including Gangs of Wasseypur, Talaash, Dekh Indian Circus and Kahaani, actor Nawazuddin Siddiqui shared the Special Jury award with maverick director Rituparno Ghosh, who was lauded for his performance in the Bengali film Chitrangada.
"It is a very important recognition for me as an actor, who has struggled for so long to find his foot in the industry. Awards are refreshing for us actors. It is good to get recognition after working so hard all year long. It instills in you a certain kind of energy to do better. I want to thank the esteemed jury members who have selected me for the prestigious honour," Nawazuddin told PTI.
Rituparno, who was awarded for his excellent grasp of the medium of cinema and his multi-faceted versatility, said, "This award has been given to non-conventional sexuality. So far people in India have started accepting it at the their individual level but this award to the subject is from the government's side."
Rituparno plays the role of a choreographer who is struggling with his gender identity in Chitrangada, a film written and directed by him.
Actor Akshay Kumar is excited about his production Oh My God, based on Gujarati play titled Kanji Virudh Kanji, winning the Best Adapted Screenplay award.
"Superb news, our first film OMG OhMyGod under @GrazingGoatPix won a National Award for Best Adapted Screenplay! Truly an OMG moment for us,(sic)" he tweeted.
Newcomer Parineeti Chopra received a Special Jury Mention for her movie Ishaqzaade.
"I never thought I would win for Ishaqzaade but when I did, it was the biggest one in the country!! That too for my first lead role! I just cannot believe it. But this scares and humbles me, and will definitely make me work even harder in the future!! Thank you jury," Parineeti said.
Director Kaushik Ganguly, whose film Shabdo won the best Bengali film award, said he is surprised that an unconventional film has got national recognition.
"The subject was unique but I am glad that the jury liked it. This is encouraging for us," he said.
Director Sujoy Ghosh won the Best Original Screenplay National award for Kahaani and the Best Editing award went to Namrata Rao for the same film.
"I am very happy winning the award. It is a huge honour. I am still trying to absorb the news. The feeling is yet to sink in," Sujoy told PTI.
Dolly Ahluwalia, who shared the Best Supporting Actress National award with Kalpana (Malayalam film Thanichalla Njan), said, "This is all thanks to my director and my audience for having faith and seeing me as Dolly Arora. For me, being happy is a small word, I am flying right now."
The actress played the role of a spunky Punjabi mother who runs a beauty parlour in Vicky Donor.
"For me this is still a dream. The National Awards have a true meaning for me and I am blessed. This is my second National award, the first was for designing costumes for Bandit Queen," she added.
Lyricist Prasoon Joshi is quite elated to have won a National award again, this time for the song Bolo Na from Bedabrata Pain's film Chittagong.
"It is a small but humble film. Also, this song was not promoted. It is an exceptionally great song and I am thankful to the jury for recognising it. Also, I have not charged anything for this song. I was moved by Bedabrata's love for cinema," Joshi told PTI.
Chittagong is directed by NASA scientist turned filmmaker Bedabrata. The 2012 film starring Manoj Bajpayee, Barry John, Nawazuddin Siddiqui and Raj Kumar Yadav is based upon actual events of India's Chittagong Uprising.
"Other film awards were not even bothered to give an award to this song. I had no clue this song would win, that too a national award. I am totally surprised for getting the award. I am much happy," he said.
Now that the song has won an award, Joshi wants everyone to listen to it.
"I just want people to listen to it and understand why it has got a national award," he said.
Joshi has earlier won a national award for penning the lyrics of Meri Maa, the song from Aamir Khan's directorial debut Taare Zameen Par.