The US Open champion, who also withdrew from the event last year, has chosen to rest his back in preparation for the upcoming Paris Masters and World Tour Finals in London, starting on 29 October and 5 November respectively.
He will be replaced as second seed by Juan Martin del Potro, who won in Vienna on Sunday and is currently trying to secure a spot in the World Tour Finals at the 02.
Roger Federer has won the title in five of the last six years.