The 24-year-old has been making steady progress up the standings since the turn of the year, and his performances at Flushing Meadows have seen him go one place higher than his previous best.
Nishikori broke into the top 10 by making back-to-back finals in Barcelona and Madrid in May, and victories over the likes of Novak Djokovic and Stanislas Wawrinka in New York have helped him return there.
His opponent in the US Open final, Marin Cilic, has also climbed the rankings after seeing off Roger Federer in the semi-finals - the Croat rising four places to world number 12, his highest position since May 2013.
Djokovic remains world number one with none of the top five changing, although two-time grand-slam winner Andy Murray has slipped to 10th after losing to the Serb in the US Open quarter-finals.
In the WTA rankings, Serena Williams tightened her grip on top spot by collecting the18th grand slam title of her career on Sunday, with the player she beat in the Flushing Meadows final - former world number one Caroline Wozniacki - returning to the top 10 in ninth place.
Li Na's withdrawal from the US Open has seen her fall to sixth, with Petra Kvitova and Maria Sharapova both moving above the Chinese.
Li's compatriot Shuai Peng was the biggest mover on Monday after her semi-final appearance in New York, the 28-year-old rising 18 places to number 21.