Rust and Bone, the dramatic and gruelling love story starring the Oscar-winning actress Marion Cotillard, has won the best film prize at the London film festival. The French-Belgian production, directed by Jacques Audiard, is the first to be honoured with the top award at a ceremony revamped this year as a more fitting finale for the annual festival.

Audiard's victory was announced by Sir David Hare, president of the competition jury, who said Audiard "has a unique handwriting, made up of music, montage, writing, photography, sound, visual design and acting. He is one of only a very small handful of film-makers in the world who has mastered, and can integrate, every element of the process to one purpose, making in Rust and Bone a film full of heart, violence and love."

Cotillard stars opposite Matthias Schoenaerts and Armand Verdure in the story of a woman who trains killer whales in a marine park before a terrible accident occurs. Guardian critic Peter Bradshaw said: "It is a passionate and moving love story which surges out of the screen like a flood tide." It marks a second victory at the London festival for Audiard, who won a prize for A Prophet in 2009.

The king and queen of modern gothic cinema, Tim Burton and Helena Bonham Carter, were among those assembled at Whitehall Palace on Saturday night.

The 54-year-old American director and his 46-year-old English muse were made fellows of the British Film Institute in a presentation by Sir Christopher Lee and Sir Trevor Nunn. Burton's new animation, the children's horror story Frankenweenie, opened the festival 10 days ago and Bonham Carter is to appear to chilling effect on Sunday as Miss Haversham in the premiere of Mike Newell's new version of Great Expectations, the closing film in the festival.

Previous recipients of the BFI fellowship include Orson Welles, Clint Eastwood, Judi Dench, Michael Caine, Ralph Fiennes and directors Danny Boyle and David Lean. The BFI chair, Greg Dyke, said: "We are delighted and honoured that both Tim Burton, one of the most creative and visionary directors, and Helena Bonham Carter, one of our finest British actresses, have both accepted BFI fellowships – the highest accolade the BFI can bestow."

Other winners included a film the judges described as "daringly vast, richly detailed". Beasts of the Southern Wild, a first feature film, was made by the 30-year-old American director and composer Benh Zeitlin, who won the Sutherland award for the most imaginative feature debut. Set on an imaginary island known as "the Bathtub", the story was inspired by flooding in Louisiana.

Awarded his latest prize by actor Helen McCrory and Hannah McGill, president of the Sutherland jury, Zeitlin has already received the Caméra d'Or award at Cannes and a grand jury prize at the Sundance film festival. "One film stood out as most clearly deserving of the top prize recognising innovation and originality," said McGill.

The Grierson award for best documentary went to the Oscar winner Alex Gibney, director and screenwriter of Mea Maxima Culpa: Silence in the House of God, a study of sexual abuse in the Catholic church. Gibney also made the 2005 Enron documentary, The Smartest Guys in the Room. Documentary-maker Roger Graef, president of the Grierson Trust jury, said: "Mea Maxima Culpa was a life-changing film made with real integrity. The use of deaf men for interviews finally telling their story was both very distinctive and respectful. The journalism showed an extraordinary paper trail of events leading right to the Vatican in an incredibly compelling manner."

The most prominent British film-maker of the night was first-time director and screenwriter Sally El Hosaini, who won the award for best British newcomer for her film My Brother the Devil. Her prize was presented by Olivia Colman and Tom Hiddleston. The prize jury president, Harry Potter producer David Heyman, said: "Sally El Hosaini's writing and direction displayed a remarkable maturity. The film transcended its genre with lyricism and tenderness and possessed a wonderful emotional truth."

Other British contenders for the newcomer category had included El Hosaini's teenage star Fady Elsayed and theatre director Rufus Norris for his film debut, Broken, along with its young star, the actress and singer Eloise Laurence.

The awards, hosted by Sue Perkins, were deliberately a more competitive affair than in previous years. For the first time shortlists were revealed. British contenders in the international lineup for best film include Ginger and Rosa by director Sally Potter and Seven Psychopaths, a comedy from the In Bruges team of Martin McDonagh and Colin Farrell.

Stars who have attended the 2012 festival include Dustin Hoffman, Winona Ryder, Billy Connolly, Dame Maggie Smith, John Goodman, Ben Affleck and the Rolling Stones.