Roger Federer said he and Rafael Nadal were still the main men in world tennis even though the Swiss lost to Andy Murray for the third time this year at the Masters Cup on Friday.

The defending champion, who was suffering the effects of a back injury and a stomach bug, lost his final group match 4-6 7-6 7-5 against Murray that ended Federer's hopes of a record-equalling fifth Masters Cup title.

Murray's victory made the Briton only the third player to beat Federer three times in one season after Argentine David Nalbandian and Spain's world number one Nadal, who has done it twice.

Despite the 21-year-old Scot now holding a 4-2 advantage in their career head-to-head, world number two Federer said his main rival would continue to be Nadal, absent in Shanghai because of injury.

"At the moment it's Rafa and myself," said the Swiss, who beat Murray in the US Open final.

"I really still feel it's that way because... we've played big events on so many occasions. I mean, we still have to play a few more grand slam finals. If that's the case, I'm very happy from my side."

Federer told reporters he was happy just to have come close to reaching the semi-finals given his physical condition coming into the season finale.

"Of course I'm disappointed. I wish I could have played the matches I played here under better circumstances," said the 27-year-old, who also lost his opening match to Gilles Simon of France.

"But I tried. I almost made a miracle happen. I can't believe how close I got, to be honest. So I'm actually very happy."