It won the best film, best actor for Farhan, as well as the best director for Rakeysh Omprakash Mehra. The movie was also honoured for best costume by Dolly Ahluwalia, best production design by Acropolis Design and best lyrics for "Zinda", penned by Prasoon Joshi.
The star-studded extravaganza, held at the Yash Raj Films studio here, also saw Sanjay Leela Bhansali's "Goliyon Ki Raasleela Ram-Leela" win big.
Deepika Padukone won the best actress trophy, while veteran Supriya Pathak was honoured for her supporting act in the movie, said a statement.
Supriya's step son Shahid Kapoor is said to have come up on the stage to especially hug her when she won the award. It was a picture perfect, according to the Facebook page of Filmfare.
The lifetime achievement award was given to veteran actress Tanuja for her outstanding contribution to Indian cinema.
The awards ceremony was hosted by "Anjaana Anjaani" co-stars Ranbir Kapoor and Priyanka Chopra. The night also saw many ravishing performances by Ranveer Singh, Priyanka and Shahid.
The best actor in supporting role was bagged by Nawazuddin Siddiqui for "The Lunchbox", which also won the best debut director award for Ritesh Batra.
Southern star Dhanush won the best debut (male) award for "Raanjhanaa" and Vaani Kapoor walked away with the best debut (female) trophy for "Shuddh Desi Romance".
The event was a truly star-studded affair with biggies like Amitabh Bachchan, Salman Khan, Rekha, Karisma Kapoor, Amrita Rao, Aditi Rao Hydari, Soha Ali Khan and Neha Dhupia, gracing the occassion.
The 59th Idea Filmfare Awards will be aired on Sony Entertainment Television Sunday.
Winners of various categories are as follows:
Best Actor in Leading Role (Male): Farhan Akhtar ( Bhaag Milkha Bhaag)
Best Actor in Leading Role (Female): Deepika Padukone (Ram-leela)
Best Film: Bhaag Milkha Bhaag
Best Director: Rakeysh Omprakash Mehra (Bhaag Milkha Bhaag)
Best Debut Director: Ritesh Batra (The Lunchbox)
Best Debut (Male): Dhanush (Raanjhanaa)
Best Debut (Female): Vaani Kapoor (Shuddh Desi Romance)
Critics Award for Best Film: The Lunchbox
Critics Award for Best Actor (Male): Rajkummar Rao ( Shahid)
Critics Award for Best Actor (Female): Shilpa Shukla (BA Pass)
The Sony Trendsetter Award: Chennai Express
The Lifetime Achievement Award: Tanuja
Best Dialogue Award: Subhash Kapoor (Jolly LLB)
Best Screenplay Award: Chetan Bhagat, Abhishek Kapoor, Supratik Sen and Pubali Chaudhari (Kai Po Che!)
Best Story Award: Subhash Kapoor (Jolly LLB)
Best Actor in Supporting Role (Male): Nawazuddin Siddiqui (The Lunchbox)
Best Actor in Supporting Role (Female): Supriya Pathak Kapur (Goliyon Ki Raasleela Ram-leela)
Best Lyrics Award: Prasoon Joshi - Zinda (Bhaag Milkha Bhaag)
Best Music Award: Jeet Ganguly, Mithoon & Ankit Tiwari (Aashiqui 2)
RD Burman Award for Upcoming New Music Talent: Siddharth Mahadevan
Best Playback singer (Male): Arijit Singh - Tum hi ho (Aashiqui 2)
Best Playback Singer (Female): Award Monali Thakur - Sawaar loon (Lootera)
Best Choreographer Award: Samir and Arsh Tanna - Lahu muh lag gaya (Goliyon Ki Raasleel Ram-leela)
Best Background Score Award: Hitesh Sonik (Kai Po Che)
Best Action Award: Thomas Struthers and Guru Bachchan (D Day)
Best Cinematography Award Kamaljit Negi (Madras Cafe)
Best Editing Award: Aarif Sheikh ( D-Day)
Best Production Design Award: Acropolis Design (Bhaag Milkha Bhaag)
Best Sound Design Award: Bishwadeep Chatterjee and Nihar Ranjan Samar (Madras Cafe)
Best Costume Award: Dolly Ahluwalia (Bhaag Milkha Bhaag)
Best VFX Award: Tata Elxis (Dhoom:3)