Not new to awards, Sen, 81, received a shawl and the recognition from Kalam at a glittering function to present the 51st national film awards at the Vigyan Bhawan here.
Sen, a critically acclaimed filmmaker, has bagged several awards at the film festivals in Cannes, Venice, Berlin and Karlovy Vary.
Besides Kalam and Sen's warm embrace, it was the long-haired president's smiling acknowledgement of singer Sonu Nigam's similar hairstyle that evoked a strong reaction from the audience.
"What an evening it was," said Kalam later. "This is the team that made us happy throughout the year, so rightfully they have been honoured."
Nigam, the winner of the national award for playback singing, motioned to his hair and Kalam's for the benefit of an amused audience.
Later he grasped fellow award winner and close friend Farah Khan - who won the award for best choreography - in a bear hug.
Among others who received awards were the makers of the rib-tickling satire "Munnabhai MBBS" and the brooding 1947 partition saga "Pinjar".
It may have lost out on an Oscar nomination despite a grand promotion campaign, but Marathi film "Shwas" by Sandeep Sawant won a befitting consolation prize in the form of the national award for the Best Film of 2003 for its moving portrayal of the relationship between a man and his grandson who is about to lose his vision.
The film's young star Ashwin Chitale shared the Best Child Artiste award with Kalidasan, who portrayed a complex role in the Malayalam film "Ente Veedu Appoontem".
Chitale, who was in Class 4 when he acted in "Shwas", won the hearts of the gathering with his traditional Marathi costume complete with headgear.
After receiving the award from the president, he was seen prancing towards his father, happily holding the certificate.
Fellow award winner Kalidasan was not far behind in attracting special attention, as he smartly extended a page to the president for his autograph after receiving the medal and certificate.
"Munnabhai MBBS", a satire on the medical profession centred on a lovable vagabond and his quirky sidekick, won the award for best popular film providing wholesome entertainment.
Rakesh Roshan's alien fantasy extravaganza "Koi Mil Gaya" bagged the award for Best Film on Other Social Issues such as prohibition, women and child welfare, anti-dowry, drug abuse and welfare of handicapped.
Malayalam film "Maargam" won the Indira Gandhi Award for Best First Film.
Manoj Bajpai won the special jury award for Best Actor for his turn in "Pinjar".
Critically acclaimed actor Gautam Ghose took home his 13th award as he received a Swarna Kamal and Rs.50,000 as Best Director for his Bengali film "Aabar Aranye", which explores human relationships.
He also won the award for best screenplay.
The top acting awards in the popular category eluded the Hindi film industry this time and regional stars walked away with more honours. Hindi actors, however, won in supporting categories.
Kerala actress Meera Jasmin received the Best Actress award for her role in "Padam Onnu Oru Vilapam", where she plays a young woman trapped in a polyandrous marriage.
Tamil star Vikram won Best Actor of the year 2003 for his powerhouse performance in "Pithamagan".
Veteran actress Sharmila Tagore, in a regal yellow sari, attracted admiring glances and resounding applause as she walked up to the stage to receive the award for Best Supporting Actress for her graceful portrayal in Ghose's film "Aabar Aranye".
Tagore, whose husband and former cricketer Mansoor Ali Khan Pataudi had accompanied her, greeted Kalam with a demure "adaab".
Another actor who evoked a thunderous applause was Pankaj Kapoor, who won the award for Best Supporting Actor for his riveting yet understated performance as a mafia don in "Maqbool", loosely based on Shakespeare's Macbeth.
The national awards acknowledged some 50 films in various languages.
The Best Music Direction award went to the popular trio Shankar Mahadevan, Aloysis Mendonsa and Ehsaan Noorani.
Tarali Sarma was named the best female singer for a song in "Akashitorar Kothale" that she rendered sans any instrumental accompaniment.
Rituparno Ghosh's "Chokher Baali" starring Aishwarya Rai missed out on the main categories but won awards for Best Feature Film in Bengali, Best Art Direction and Costume.
President Kalam later advised the film fraternity to contribute in building the society by making meaningful cinema that depicted the fight against corruption.