The semi-final had been controversially suspended overnight on Friday with Djokovic complaining about the "extreme wind" in the stadium.
However, it's 25-year-old Austrian fourth seed Thiem who goes on to face Nadal where he will be buoyed by having defeated the 17-time major victor four times on clay in his career. "Both of us, we could win, and I luckily got the better in the end".
Djokovic levelled at 5-5 with considerable help from Thiem but for the third time in the set he came unstuck serving into the wind, seeing his winning grand slam run ended at 26 matches.
But Thiem regrouped. It was Djokovic who faltered - and who lost, something he hadn't done on a Grand Slam stage since the 2018 French Open quarterfinals.
Thiem was ahead in fourth set too, but Djokovic came from behind and claimed the fourth set to push the match in fifth round. Rafa Nadal goes in search of his 12th French Open title but don't count out Novak Djokovic.
"Huge shout out to Leylah Annie Fernandez for winning the French", said Shapovalov on Twitter.
The top-seeded Fernandez beat eighth-seeded Emma Navarro of the USA 6-3, 6-2.
Should he fail - which seems likely - the 25-year-old Thiem will be back.
Mostly, though, because Dominic Thiem managed to outperform Djokovic at his own brand of defense-to-offense, speed-and-power baseline game.
Thiem broke to move into a 4-1 lead and then had a point to lead 5-1, which Djokovic saved with a forehand.
Nadal played his last-eight match against Kei Nishikori on Tuesday and completed his straight sets semi-final win over Roger Federer by the middle of Friday afternoon. Austria's Dominic Thiem reacts after his semifinal match against Serbia's Novak Djokovic.
They are slated to open Saturday's schedule in Court Philippe Chatrier at Roland Garros. The over-under on sets is 3.5 and Nadal is favored by 6.5 games in the latest Nadal vs. Thiem odds.
"I'm happy that Denis, Felix, Bianca are able to do everything great and it motivates me to do better for the next couple of years and for the future", said Fernandez, who also reached the Australian Open girls' final earlier this year.
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Barty reaches first Grand Slam singles final
While this was not the final many would have predicted, it was a meeting between two of the most in-form players of 2019. Coverage: Live text and radio commentary on selected matches on the BBC Sport website and app.