Djokovic leads 6-4, 3-6, 7-6 (9) after saving three set points in the tiebreaker.
After the epic six hours and 36 minutes semi-final encounter won by Kevin Anderson over John Isner, Spanish second seed Nadal did not hit the first serve of his match against 12th-seeded Djokovic until 8.09pm.
In the end, and to the surprise of no one, they did not come close to finishing after two hours and 54 minutes of play on Friday night.
"I don´t really know what to say right now, playing like that in those conditions was really tough for the both of us", said eighth seed Anderson.
"If I had been on the opposite side, I don't know how you can take that, playing for so long and coming out short".
"So I apologise if I'm not more excited right now because the mix of emotions getting through something like that is quite different".
It is absolutely evident that Djokovic has an edge over his Spanish rival on grass courts over various time-frames, and with the nearly five-hour quarter-final for Nadal factored in as well, the available [2.00] looks worth recommending to me. Anderson then took the fourth set 6-4, breaking the Isner serve twice in the set.
Steve Tignor previews the men's semifinals at Wimbledon.
The final set alone lasted two hours and 50 minutes. But Anderson roared back, outlasting the great Swiss to win 2-6 6-7 7-5 6-4 13-11. Watch Nadal vs Djokovic live stream online on ESPN TV this morning at 11 am EST / 8 am PST for what could and hopefully will be a five set marathon to determine the victor.More news: JUST IN: Chelsea Sack Conte, Appoints Sarri As New Manager
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All the 32-year-old had left in him was to give Isner a sympathetic hug after he came out on top in the second-longest match ever contested at the All England Club.
But they had not shared a Grand Slam stage since Djokovic inflicted a bitter defeat on Nadal at Roland Garros in 2015.
But that break in the eighth game of the third set did not hurt anything like the moment when he finally slapped a tired forehand wide at 7.46pm local time to surrender his title hopes.
Anderson is the first South African to make the last four since Kevin Curren in 1983.
After that, each continued to hold serve and did so for 48 games in the final set. Anderson fell to his backside trying to return an Isner serve, but got to his feet with his racket in his off hand.
However, I am utterly shocked that the markets are finding it hard to split Nadal and today's opponent, Novak Djokovic, for the second semi-final, which will commence no earlier than 1500 United Kingdom time.
Their 12-year rivalry stands at 26-25 in favor of Djokovic, but those numbers don't reflect the topsy-turvy nature of the on-court relationship between the Spaniard and the Serb.
From 2011 through 2016, Novak Djokovic was a mainstay in Grand Slam semifinals, advancing at least that far in 22 of the 24 majors (and winning 11) over that span. He has one Slam final appearance in that span.
Isner's grass data over the last two years is also marginally better than Anderson's, so he does look to hold a slight edge in his quest to reach his first ever Grand Slam final.