The 15-time Grand Slam champion, who had not reached a semifinal match since claiming the Australian Open in January, topped Thiem for his third Madrid trophy and 33rd Masters 1000 to tie Nadal for most ATP Masters won.
Djokovic secured his first final appearance since winning the Australian Open at the start of the year by beating Dominic Thiem 7-6 (2) 7-6 (4).
No. 6 seed Kai Nishikori also progressed after a 7-5, 7-5 victory over Hugo Dellien in a match that lasted for just over two hours, but No. 7 seed, Juan Martin del Ptro was beaten 6-3, 2-6, 7-5 by Serbia's Laslo Djere.
Nadal, meanwhile, was left reflecting on a third straight semi-final exit on clay after losing to Fabio Fognini in the Monte Carlo Masters and Dominic Thiem in the Barcelona Open.
"He knew I had a tough match last night, so he took advantage...[made] me run and suffer more and I just didn't have solutions". And yes, he played quite smart. The two exchanged two more breaks late in the set, and Djokovic eventually prevailed in the deciding tiebreaker.
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Tsitsipas was impressed with how Djokovic wrapped up the win in 91 excruciating minutes.
Revealing his long-term focus was "to be fit, play properly and have a high tennis level", he said: "If I manage to do that, I will have a good opportunity to fight for titles for the rest of the year".
Kiki Bertens won the women's title on Saturday. "You've been great, I love you".
"I couldn't keep playing at the level that I wanted, but I'm very happy and very proud of my career", Ferrer said. "I've been really close, but I haven't been able to win".
While I've discussed the head to head meetings as being largely irrelevant, it does add insight into how much Tsitsipas needs to improve if he is to test Nadal tonight.
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I anticipate the match to be very competitive, and the market does too, chalking up Djokovic as a marginal [1.90] favourite.
Djokovic, victor in Madrid in 2011 and 2016, was fully rested after his quarter-final opponent Marin Cilic had withdrawn because of food poisoning, while Thiem had to dig deep to beat Roger Federer in a gruelling three-setter.
"He deserved the victory", said Tsitsipas of Djokovic after his 6-3, 6-4 defeat.
Instead of celebrating titles and records, Nadal is having to explain why he has struggled to win matches. I felt I was dictating the play and played my best tennis so far this week. This is the first time since 2004 that Nadal arrived in Madrid without a title. "I mean, we can both lose before finals", said Djokovic on their chances of clashing in Paris.
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