Nadal, 26, hopes to be back to full fitness in time for the Australian Open in January.
The Spaniard, whose athletic, aggressive playing style places huge demands on his muscles and joints, has been sidelined several times by knee problems during his 11-year career.
His latest injury was diagnosed as a partial tear of the patella tendon and an inflammation of the Hoffa's fat pad and after the shock defeat at Wimbledon he was unable to defend his Olympic title at the London Games.
As well as the US Open, which he won in 2010 and lost to Novak Djokovic in the final of 2011, Nadal missed the season-ending Tour Finals and Spain's Davis Cup final defeat to Czech Republic at the weekend.
His absence deprived tennis's "big four" of Nadal, Djokovic, Roger Federer and Andy Murray of one of its most competitive and successful members for the second half of the season.
Nadal had played some of his best tennis in the first six months of 2012, losing narrowly to Djokovic in the final of the Australian Open and winning a record seventh Roland Garros title on his favoured clay.