Kapadia's Oscar nominated film beat "Cartel Land", "He Named Me Malala", "Listen to Me Marlon" and "Sherpa" to win the honour.
The filmmaker in his acceptance speech paid tribute to the tragic star, who died in 2011 at the age of 27, following a battle with drug and alcohol.
"We really fell in love with her when making the film and our aim and mission was really to try and tell the truth about her.
"To show the world what an amazing person she was, how intelligent, how witty, how beautiful she was, before it all kind of got out of control and went a bit crazy," Kapadia said referring to the tabloid circus around Winehouse's life.
It is Kapadia's third trophy at the British Film Awards. He previously won for sports documentary "Senna" in 2012 and Irrfan Khan-starrer "The Warrior" in 2003.
The 44-year-old filmmaker, later, took to Twitter to thank the crew of the film.
"Thank you to all of the crew and all of our contributors who trusted in us #AMY #EEBAFTAs @AmyFilmUK @AmyTheMovie.
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