World number one Simona Halep, the runner-up in 2014 and 2017, routed Belgian 16th seed Elise Mertens 6-2, 6-1 to reach the French Open quarterfinals for the third time.
When Schwartzman broke in the third game of the second set, the alarm bells were ringing in the Nadal camp and although he quickly levelled he was immediately broken again.
Rafael Nadal has lost his first set at the French Open since 2015.
Marterer may have felt he would need a degree of fortune to have any chance of an upset and the early signs were promising as a net cord set up two break points, Nadal double faulting on the first to hand his opponent a 2-0 lead.
Nadal had to receive treatment to his wrist at the end of the set with extra strapping applied.
The victor will face either Juan Martin del Potro or Marin Cilic, who were locked at 5-5 in a first-set tiebreak.
He may have halted the mutiny for now but Nadal was strangely off-colour, unable to dictate the rallies as he usually does on clay.
Nadal, returning with his famed forehand finally firing on all cylinders, earned back-to-back breaks to move within a hold of the set.
Breaks were swapped twice in the first set before 25-year-old Schwartzman broke the Nadal serve for a third time to lead 5-4. And previous year, he earned the trophy without dropping a set.
More important than that, of course, is the match's ultimate outcome, and a significant moment came with Schwartzman serving while up 3-2 in the second after the initial delay.
At one point Nadal, the reigning champion and 10 times victor, found himself a set and a break down to the diminutive Argentinian Schwartzman.
Nadal pumped his fist and yelled: "Vamos!".
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