Nadal won 6-2 4-6 6-2 7-6 to advance to the final four.
The 13-time Roland Garros champion will meet Germany's Alexander Zverev for a place in Sunday's final.
Djokovic beat Nadal in the semi-finals last year which was just his third ever loss at the tournament.
Meanwhile German third seed Alexander Zverev capitalised on an error-filled performance from Carlos Alcaraz to tame the high-flying teenager.
