Hamit Altintop won the Puskas Award for Goal of the Year for his wonder volley when Turkey played Kazakhstan, Brazilian striker Marta won the Women's Player of the Year for a fifth consecutive time and Germany's Silvia Neid won the Women's Coach of the Year.
The last player to win the Ballon d'Or award twice in a row was Dutch striker Marco van Basten in 1988 and 1989, while Messi's former Barca colleague Ronaldinho won the Fifa prize in 2004 and 2005.
Many thought Iniesta, who scored the winning goal as Spain beat Netherlands 1-0 in the World Cup final in Johannesburg in July, and Xavi, who was the lynchpin of the Spanish side, were favourites to win at a glittering ceremony in Switzerland.
But Messi scored a remarkable 60 goals for club and country in 2010 and is widely regarded as the most gifted footballer of his generation.
The only Spanish winner of either prize was Luis Suarez who won the Ballon D'Or in 1960.
The coaching prize is the latest accolade in a glittering career for Mourinho, who has won league titles in Portugal, England and Italy.
"The most important things for me are the collective titles, not the individual ones," said Mourinho, who left Inter to join Real Madrid in the summer.
The Ballon d'Or is awarded based on votes cast by journalists from around the world, as well as coaches and captains of national teams.
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