Monday's new ATP rankings put the Swiss back in front of Britain's Andy Murray, the player he defeated in the semi-finals in Cincinnati.
It means Federer, 34, who last won the U.S. Open in 2008, cannot meet world number one Djokovic until the final.
Richard Gasquet of France went up one place to number 12, replacing American John Isner, but the biggest mover was Feliciano Lopez of Spain, up five places to number 18.
(Reporting by Steve Tongue, editing by Tony Jimenez)
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