The movie, which has won three Oscars and three BAFTAs, lifted the prize at last night's ceremony at the BFI Southbank in London.
Director Guillermo del Toro flew from Paris to collect the award from actress Catherine Deneuve.
He said: "I am very humbled by the competition and the nominations so I am very happy to have won this award. I am extremely thankful because world cinema seems to be not only about geography of the world out there, but about charting the world within us.
"Very often people think that the only way to tell the truth is through reality. So I find, by my own experience, irreality is sometimes a better tool to tell the truth."
The movie was chosen from a shortlist of five by a panel consisting of actor Christopher Eccleston, documentary-maker Nick Broomfield and actress Archie Panjabi.
It beat Oscar-nominated drama The Lives Of Others, as well as The Science Of Sleep, Climates and Syndromes And A Century.