The two-time victor will meet Novak Djokovic in the last four on Friday.
That mishap could not stop Nadal from reaching his sixth Wimbledon semi-final and he celebrated the moment by raising both arms up into the skies after four hours and 48 minutes of thrilling action.
Rafael Nadal of Spain celebrates winning his men's singles match against Czech Republic's Jiri Vesely, on day seven of the Wimbledon Tennis Championships, in London, Monday July 9, 2018. Del Potro broke and served for the set at 5-4, but double-faulted and Nadal clinched the break-back with a rasping forehand down the line.
While the Federer exit, to South African Kevin Anderson, losing 13-11 in the final set, is what will sadden most viewers and grab what there are of tennis headlines today, Nadal coming from two sets to one down against perennial almost man Juan Martin Del Potro produced perhaps the most awesome tennis of the day, and definitely the moment of the tournament.
Nadal has 17 while Djokovic has stalled on 12 since completing the career Grand Slam at Roland Garros in 2016.
"Well, at the moment I´m feeling sad after nearly five hours of running and playing this high level against the No. 1 in the world and losing", added Del Potro.
The deciding fifth set was a tight battle, but in the fifth game, Nadal got the solitary break to lead 3-2.
Del Potro, who'd saved four set points, grabbed one of his own on Nadal's serve and levelled at a set apiece with a forehand that clipped the net and fell inside the service box. The hard-serving American beat Milos Raonic of Canada 6-7 (5), 7-6 (7), 6-4, 6-3 to set up a meeting with Kevin Anderson of South Africa in Wimbledon's last four.
Former US Open champion Del Potro then stunned the Spaniard with the only break of the third set in the 10th game, secured with a deep forehand.
Del Potro too noted the change in conditions but appeared to relish the chance to slide around a bit more on the grass.
Nadal caught Del Potro napping in the fifth game of the fourth set, breaking him to love to lead 3-2.
"Against Rafa", del Potro said, "you must go for winners all the time". Raonic hit 31 aces to Isner's 25 but was broken three times, including the last game of the match.