Nadal played with knee strapping on his right leg against Federer and hinted he would pull out of Basel after the Shanghai Masters final loss.
Meanwhile, Maria Sharapova has been knocked out of the Kremlin Cup in the first round.
Federer is mathematically able to catch Nadal and could become the number one ranked player for the first time since 2012.
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.
It was the 24th meeting in a final between the world's top two, and with the roof again closed because of rain in Shanghai, Federer built a 4-2 lead en route to winning the opening set.
"I want to send a special message to the many tennis fans in Switzerland which have always showed great support and respect also on my matches with Roger", Nadal said.
"Hope to see you next year".
Federer put on a masterclass to beat Nadal 6-4, 6-3 on Sunday, the 36-year-old lifting his sixth trophy this season and underlining a turnaround in fortunes against his long-time nemesis. Nadal would be playing in Switzerland where his five-match losing streak to Federer began in the 2015 final.
Sharapova, meanwhile, lost 7-6, 6-4 to Slovakia's Magdalena Rybarikova in her first match in Russian Federation since returning from a doping ban this year.
While Federer is best on fast surfaces and more rested with 48 total matches played in 2017, Nadal has logged 75 total matches with his more grueling baseline tactics.
"World number one I don't think will happen but if I play like this maybe I'll get close, who knows?"
The win in China was her first title since serving a 15-month doping ban and lifted her 29 places in the world rankings to 57th.
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