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More than an hour after the women's final should have started on another stormy day on Court Philippe Chatrier, fourth seed Thiem thumped a forehand winner past Djokovic to seal victory 6-2 3-6 7-5 5-7 7-5 on Saturday after squandering two earlier match points.
It snapped Djokovic's 26-match winning streak in Grand Slam matches and ended the Serbian's hopes of holding all four of the sport's major prizes simultaneously for the second time, having achieved it by winning his only French Open in 2016.
Djokovic, who had trailed 6-2 3-6 3-1 overnight after the semi-final had been curtailed on Friday because of rain and wind, had won his previous 10 Grand Slam semi-finals.
The world No 1 had looked serene throughout the fortnight, not dropping a set, but in "hurricane" conditions he described as the "worst he had ever played in" he was blown off course by the ferocious hitting of Thiem.
The 25-year-old, who lost to Nadal in last year's final, handled the elements better as he kept alive his dream of winning a first major title when he takes on the 11-times champion again on Sunday.
"If you reach the final here it's always against Rafa," Thiem said on court. "It was an amazing experience last year and I will try everything to be better this year."
Thiem said he had no complaints that the match had been stopped on Friday with the wind strength increasing and a forecast for more rain to come.
The second stanza of the match began in teasing winds that often played tricks with the ball, yet the quality of the tennis produced was often scintillating.
Djokovic got straight into his groove and broke back in the third game of the day. He was denied another break at 4-4 when Thiem failed to put away two smashes but then got an outrageous net cord off an audacious half-volley.
Under pressure in the 12th game Djokovic was given a time violation before saving three set points, one with an ace.
But a sensational forehand pass by Thiem gave him a fourth set point which he converted when his dipping backhand forced a volley error from Djokovic.
Djokovic, still annoyed by his time violation, erupted furiously at the umpire and was given a warning for unsportsmanlike conduct.
The 15-times Grand Slam champion regained his composure, however, to break serve twice in the fourth set but on both occasions the attacking Thiem hit back immediately.
Thiem double-faulted at 5-5 to gift Djokovic another break and this time the Serbian made it stick to take the match into a decider.
The fifth set was as wild as the weather.
Thiem broke to move into a 4-1 lead and had a point to lead 5-1, which Djokovic saved with a clubbing forehand.
Seconds later a howling rain squall sent the players off court for more than an hour and when they returned Thiem looked poised to win when serving at 5-3 and 40-15.
He crumbled, however, gifting Djokovic four points in a row and his chance appeared to have gone when Djokovic made it 5-5.
Somehow he put that behind him, though, and when Djokovic served at 5-6 he was the one who buckled.
Two tight forehands thumped into the net to give Thiem a third match point and this time the Austrian hammered home a forehand to spark celebrations in his coaching box.
"It was an epic match," claycourt warrior Thiem, who also beat Djokovic here in 2017, said. "Somehow I had the feeling that I had the lead in the whole match.
"I luckily got the better in the end."