His three-set victory over Zverev also sent the 19-time grand slam champion soaring above Tiger Woods as sport's all-time highest prize money earner with a mind-boggling $US110,340,682 ($A145,180,678).
Nadal joins Andy Murray, Novak Djokovic, Stan Wawrinka, Kei Nishikori and Milos Raonic on the sidelines but Federer believes the game's injury epidemic simply comes down to age. "It's been a tough group so to be through in two matches is great", Federer said.
"It was not easy for me to lose my serve at the start".
The Spaniard has never won the season-ending tournament and was determined to rectify that but during the 157-minute epic against Goffin it became obvious he was playing through large amounts of pain. He's in the semifinals.
"But I am really not ready to play, no?"
'I think you can't put them all together.
Zverev might rue missed opportunities, having squandered a set point and 4-0 tie-break lead in the first set, but it was concentration and stamina that ultimately proved the difference.
The 36-year-old was broken twice during the match and was forced into a deciding third set for the first time this week, but backed up his opening-day success over Jack Sock with another impressive performance.
From there on it was all Federer. I felt I could have played more.
Federer's list of titles this year is already extraordinary - Melbourne, Indian Wells, Miami, Halle, Wimbledon, Shanghai, Basel - and he is well placed to add another after his three-set victory over 20-year-old Alexander Zverev on Tuesday, which made him the first man into Saturday's semi-finals.
The No. 8-seed, who seized qualification by winning the final Masters event of the season in Paris, lost his debut match to Federer, but he is now 1-1.
"I think I was able to stay the course and use my slice quite effectively, then try with variation to go into his forehand", Federer said.