93-year-old Pran could not attend the ceremony due to his ill health but a documentary on his life and work was received with a standing ovation by the audience.
Pran, best known for his portrayal of negative roles in Hindi movies like 'Milan', 'Madhumati' and 'Kashmir Ki Kali', will be later honoured with the Swarna Kamal (golden lotus) medallion, a cash prize of Rs 10 lakh and a shawl.
'Paan Singh Tomar', a biopic on an athlete-turned-dacoit, won the best picture award. The best film trophy comes with a Swarna Kamal and a cash prize of Rs 2,50,000.
Talking about the film's extraordinary journey, director Tigmanshu Dhulia told PTI that it was special to get the award on a day when Indian cinema is celebrating 100 golden years.
"It has turned out to be a very special film. When I was making it, I did not think that it would turn out to be a pathbreaking film. It is a very proud moment for us," Dhulia said.
Irrfan shared the best actor trophy with veteran Marathi actor Vikram Gokhale for his role in 'Anumati'.
Actress Usha Jadhav was given the best actress trophy for her portrayal of a rustic housewife in Marathi film 'Dhag'.
The best actor and actress award comes with a Rajat Kamal and Rs 50,000 cash prize. Dhag's director Shivaji Lotan Patil won a Swarna Kamal and Rs 2,50,000 for the best director award.
Bollywood added glamour to the ceremony with actor John Abraham, Parineeti Chopra, Irrfan Khan and Nawazuddin Siddiqui turning up for the event.
Produced by Abraham, "Vicky Donor" won three trophies. It was the joint winner with Anwar Rasheed-directed Malayalam film 'Ustad Hotel' for the best popular film providing wholesome entertainment honour. Both the films received Swarna Kamal and Rs 2,00,000.
Best supporting honours went to 'Vicky Donor' actors Annu Kapoor and Dolly Ahluwalia who shared the award with Kalpana for Malayalam film 'Thanichalla Njan'.
"2012 was a very good year for quality films so it is great to see your film win three national awards. The film was based on an unusual subject of sperm donation which is not discussed openly but the jury loved the film. It is also special to get the award from the President as I always wanted to meet him," film's director Shoojit Sircar told PTI.
Bedabrata Pain's much-lauded movie 'Chittagong' shared Indira Gandhi award for best debut film with Siddhartha Siva's Malayalam film '101 Chodiyangal'. Both the films were given Swarna Kamal and Rs 1,25,000.
Director Sujoy Ghosh won the best original screenplay award for his Vidya Balan-starrer 'Kahaani' while another Hindi film 'Oh My God' won the best screenplay for Bhavesh Mandalia and Umesh Shukhla.
'Ustad Hotel' was recognised for best dialogue for Anjali Menon. Each winner was given Rajat Kamal and Rs 50,000.
'Kahaani's Namrata Rao was given the trophy for best editing. She also received Rajat Kamal and Rs 50,000.
Singer Shankar Mahadevan and lyricist Prasoon Joshi were given the award for best male playback singing and lyrics in "Chittagong". Shankar also performed his award winning song at the ceremony.
Aarti Anklekar Tikekar, the best female playback singer for 'Palakein Naa Moondoon' from Marathi film 'Samhita', also mesmerised the audience with the beautiful recital of the song.
Malayalam film 'Thanichalla Njan', apart from fetching the supporting actress for Kalpana, was also awarded in the Nargis Dutt award for best feature film on national integration category. The winner was given a Rajat Kamal and Rs 1,50,000.
Malayalam film 'Spirit' was given the award for best film on social issues.
Another Malayalam film 'Black Forest' was given the award for the best film on environment conservation/preservation.
Hindi film 'Dekh Indian Circus' was the best children's film and its lead actor Virendra Pratap shared the best child actor honour with '101 Chodiyangal'. Nikhil Advani-directed 'Delhi Safari' was awarded the best animation film.
Pandit Birju Maharaj accepted the trophy for best choreography in Kamal Haasan's 'Vishawaroopam' which also won the best production design award.
Poornima Ramaswamy took home the best costume designer trophy for Tamil film 'Paradesi' while Raja won the best make-up artist award for Tamil movie 'Vazakkuenn 18/9'.
Bollywood dominated in the special jury award with Nawazuddin Siddiqui winning the special mention for his role in Anurag Kashyap-directed 'Gangs of Wasseypur', 'Kahaani' and 'Dekh Indian Circus' with director Rituparno Ghosh for his Bengali film 'Chitrangada'.
Best cinematography honour went to 'Ko:YAD', a film in Mising language.
Best audiography award was shared by Malayalam film 'Annayum Rassoolum', 'Shabdo' and 'Gangs of Wasseypur'.
Malayalam film 'Kaliyachan' and Marathi film 'Samhita' shared the best music direction award. Telugu film 'Eega' was given the trophy in the best special effects category.
Special mention was given to actor Lal for Malayalam film 'Ozhimuri', H G Dhattatreya for Kannada film 'Bharat Stores', Parineeti Chopra for 'Ishaqzaade', Bishnu Kharghoria for Assamese film 'Baandhon', Tannishta Chatterjee for Hindi film 'Dekh Indian Circus', Hansraj Jagtap for Marathi film 'Dhag' and late actor Thilakan for Malayalam film 'Ustad Hotel'.
'Silent Cinema In India-A Pictorial Journey' in English by B D Garga won the National award for the best book on cinema while best film critic award went to Malayalam writer P S Radhakrishnan. Piyush Roy won a special mention.
Non-feature film awards were also given in 19 categories.