Federer, who has won the last five encounters between the pair dating back to the 2015 Basel final, also beat Nadal in the Australian Open final, a round of 16 match at Indian Wells and the Miami final this year.
“Have been a very difficult match for me,” Nadal said. “He played very fast and he played well.”
Despite his dominance in 2017, Federer, 36, does not rate his chances of catching Nadal in their head-to-head record.
“It’s not going to happen,” he said. “We don’t have enough years left on the tour.”
He added: “You can’t win them all against Rafa, to be honest. He’s too good of a player.”
The Shanghai Masters is Federer’s 94th career title, moving him into a tie with Ivan Lendl in second place on the Open era list.
Nadal arrived on court with a bandage under his right knee, the same leg he twice smacked with his racket after losing his serve for the first time this week in the semifinal against Marin Cilic.
Federer said he was surprised to see the wrap and did not feel Nadal was struggling with his movement.
In his postmatch news conference, Nadal elected not to discuss the knee injury, saying, “I don’t want to talk about that now, sorry, but after losing final is not the moment.”
When asked if he would play coming tournaments in Basel, Switzerland, and Paris, Nadal refused to confirm his participation.
Federer took advantage of a third break point in the first game of the match with a winning backhand passing shot. He broke Nadal’s serve again on a second break point in the fifth game of the second set when Nadal sailed a backhand crosscourt wide. In the final game, Nadal netted a forehand at 15-40 to end the 72-minute match.
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