The Brazilian marches on after an epic five-hour battle with the Serb, the former world number one. Jannik Sinner is also out of the French Open.
Even if Novak Djokovic is a long way from his best form, his defeat to Brazilian João Fonseca at Roland Garros still comes as a surprise.
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Fonseca will face Norway's Casper Ruud in the fourth round following an epic battle against the Serb that lasted more than five hours.
Djokovic looked to be on course for victory after taking the first two sets of the match 6-4, but the Brazilian turned the contest on its head with a 6-3 win in the third set. He then went on to take the fourth and fifth sets 7-5.
Brazil has not had a major tennis figure since Gustavo Kuerten, the former king of clay and winner of the 1997, 2000 and 2001 editions of the French Open.
Djokovic is not the only big name to fall in the early rounds of this year's tournament.
Italian Jannik Sinner, the current world number one, was knocked out by Argentina's Francisco Cerúndolo, after becoming unwell in the heat. The world number one was clearly struggling in the last two sets, both won 6-1 by Cerúndolo, who chose not to celebrate his victory as a mark of respect for his opponent.
The Italian must therefore put his Grand Slam dream on hold. Sinner came into the tournament on the back of an impressive 30-match winning streak.