The show, initially hosted by Bollywood superstar Salman Khan, was extended for a month with director Farah Khan taking over the duties of the host.
Farah handed the trophy and Rs 50 lakh as prize money to Gautam.
"I cannot believe that I have won. It has been an exceptional journey with plenty of ups and downs but it is an experience that I will cherish for the rest of my life.
The 27-year-old actor beat Karishma Tanna, Pritam Singh, Ali Quli Mirza and Dimpy to become the winner of the longest season of the controversial reality show that has celebrities holed up inside a house with cameras watching their every move.
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Ali and Dimpy became the first two champions to be evicted on the finale, leaving behind Gautam, Karishma and Pritam in the race.
The top three finalists were then offered an amount of Rs 25 lakh and an option to quit the game. RJ Pritam accepted the offer and exited the show.
Finally Gautam was declared as the title-holder, with Karishma finishing as the runner-up. Interestingly, both started out as enemies on the show, when it began but developed a cordial relationship in the last few weeks.
Dimpy was the first to get evicted with Bollywood actress Sonakshi Sinha taking her out of the house after grilling all the finalists.