Tsonga suffered an early blow in the first set as Nishikori swiftly went a double break up in France, with the home favourite struggling to find his feet.
The 29-year-old created just one break-point opportunity throughout the entire set as he lost serve once again and Nishikori claimed the lead.
The Japanese pro struggled to bring his lethal edge into the second set as Tsonga was stronger on his service games, the third of which he saved four break points in.
Tsonga took the only break of the second set to draw level and push the contest into a decider in Paris.
Both competitors held serve well, but it was Nishikori who found the breakthrough to snatch the win and progress into the final eight.