The unexpected ending brought an end to a scrappy match that had already lasted three hours and 13 minutes without the second set being concluded.
Nadal, who continues to battle a chronic foot injury, was far from his best in the opening set but showed his brilliance in the crucial moments to help win it.
The 21-time Grand Slam champion walked out to the match amid huge applause, before the crowd serenaded him with a rendition of 'Joyeux Anniversaire' - 'Happy Birthday' in French.
The party atmosphere quickly changed. Zverev broke Nadal's serve in the opening game of the match, with Nadal struggling on the slower conditions in humid conditions under the Chatrier roof on a rainy Paris afternoon.
Zverev moved 4-2 ahead with a service hold to love, showing his high level of confidence with powerful winners.
But he got tight when serving at 4-3 and Nadal broke as part of a run of three successive games that left Zverev serving to stay in the opening set.
The German came under pressure again, fending off three set points which his errors had helped create. But he survived, although he was then unable to take either of two break points himself in the 11th game.
It was left to a tie-break to separate the pair, where Nadal produced two forehand winners at crucial times that were almost unworldly.
Nadal saved Zverev's third set point with a whipped crosscourt forehand which left most in the crowd in awe and jubilantly celebrating, sealing the set at the sixth opportunity with a sensational forehand winner down the line.
A messy second set featured eight breaks of serve in the opening nine games. Nadal finally held serve for the first time in the set for 5-5 and another tie-break was necessary until agony struck for Zverev.
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