The Japanese eighth seed had to call on the trainer to have his chest massaged early in the third set. Despite that setback, he dug in to ensure he did not have to stay on court longer than necessary, wrapping up the win with a backhand winner.
He will next take on South Korea's Chung Hyeon.
Chardy won the first game on Nishikori's serve but Nishikori immediately broke back and quickly found his stride.
The Japanese, who reached the Roland Garros quarter-finals in 2015, bagged 12 consecutive games as he went from 3-3 in the first set to 3-0 in the third, when he had to take the injury time out.
He lost momentum upon resumption as Chardy broke twice to force a tiebreak.
However, once in the tiebreak Nishikori kept his wits and converted his first match point.
(Reporting by Julien Pretot, editing by Pritha Sarkar)
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