The Serbian tennis player will now proceed to a final bout against South African tennis player Kevin Anderson.
He also said his semi-final should have been played before the Anderson-Isner match on Friday.
And he made it clear Grand Slam tournament organisers should consider a rule change - perhaps introducing a tie-break at 12-12 - to make the deciding set of five-set matches less gruelling.
Nadal and Djokovic's semi-final could not be completed before the 11pm curfew last night, so had to be finished today.
Novak Djokovic says he has "not much to lose" when he goes for his first Grand Slam title in nearly two years against Kevin Anderson in the Wimbledon final. "I have to say congratulations to John on a great tournament and hopefully he can come back stronger". "I can feel the crowd (get) pretty antsy for us to get off the court".
Djokovic led 5-3 but Nadal won a 23-stroke exchange with a dropshot to lead 6-5. Their final set alone lasted almost three hours.
"It makes it even better for me, makes it even more special because I managed to overcome challenges and obstacles, to get myself to the final of a Slam", he said.
As intense as any athletes in any sport, these two didnt exactly slowly ramp things up when they returned to Centre Court about 14 hours after theyd departed.
The 12-time grand slam victor will compete against South African eighth seed Anderson, who plays in his second major final, at 2 pm (1200 GMT) on Sunday.
He said he worked hard to stay calm like the master of tennis cool Roger Federer, but it was tough because of the high level and intensity of the match and the quality of his opponent.
Djokovic hasnt won a major in more than two years, dealing with an injured right elbow that was so painful in 2017 he quit his quarterfinal at Wimbledon and sat out the rest of the season. It was the longest men's semifinal in Wimbledon history at six hours and 36 minutes.
That match will be played with the roof open.
Anderson had break points in the 15th, 21st and 35th games of the decider before taking victory when a tired Isner hit long.
Fans in stands expressed due appreciation for Isner and Anderson's effort and skill - to a point.
When Nadal broke in Saturday's second game, a dismayed Djokovic grabbed a spare ball and whacked it with his racket against the wall behind the baseline.
Each time one broke serve, the other broke back, resulting in yet another 6-6 deadline that extended play. The penultimate of those ultimately helped him to the only non-tiebreak victory of the first four sets, and the last allowed him to finally get a leg up on Isner in the final stanza.
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