The 29-year-old had been linked with a move to the west London side throughout the summer, with West Brom also rumoured to be interested in his services.
Reports had initially suggested that Martin Jol had failed with a bid for the Ghana international, but the Cottagers did eventually agree a deal earlier on deadline day.
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He wrote on his Twitter account: "Deal with @fulhamfc is off."
Boateng, who can play as a defensive midfielder or at centre-back, could have helped to fill the void left by the likes of Dickson Etuhu, Mousa Dembele and Danny Murphy, who have all left the club this summer.
Fulham have already been busy in this summer's transfer window, adding Dimitar Berbatov, Hugo Rodallega, Mladen Petric, Sascha Riether and Kieran Richardson to their ranks.
However the club have seen one of their stars from last year leave in Dembele, who completed a move to White Hart Lane, while Clint Dempsey is also seeking a move away from the club but rejected an offer form Aston Villa.