"I sadly announce that I have to pull out of the Swiss Indoors Basel, after seeing my doctor in Spain", he wrote.
In these circumstances, Nadal and Federer had another blockbuster of their own last Sunday in the Shanghai Rolex Masters [VIDEO]' final.
Federer has triumphed seven times in his hometown event and will close the gap on Nadal to 1460 points with a title in the race to the year-end number one.
With the ATP Finals coming up next month, Nadal said on his Facebook page he had made the decision to pull out of next week's Basel tournament after getting medical advice.
The Spaniard, 31, says he is suffering from an "over-stressing of the knee", and has been advised by his doctor to take time off.
Av16 match winning streak on the hard took its toll as Nadal's late surge in the US Open, Beijing and Shanghai nearly secured his seat.
"I want to send a special message to the many tennis fans in Switzerland which have always shown great support and respect also on my matches with Roger". But, for a guy who used to suffer from tendinitis in his both knees, it's no surprise at all.
For now, Nadal and Federer are slated to play all three events, with Basel beginning next week. Once again, an inspired Roger Federer cruised past Rafael Nadal [VIDEO] for the fourth time this season. This past weekend, Federer extended his winning streak over Nadal to five matches after beating the Spaniard in straight sets to win the Shanghai Masters.
Nadal and Federer have each won six titles this year, splitting the four grand slams between them.