Local favourite Paire's lack of focus was the key to a match that was interrupted by failing light on Sunday, as the Japanese seventh seed set up a meeting with 11-times champion Rafa Nadal.
The match resumed on Court Suzanne Lenglen at two sets to one, with Paire taking command in the fourth with an early break.
He then wasted a chance to get another break and Nishikori eventually forced a tiebreak only to get tight-armed, wasting two match points on serve before conceding a set point with an ugly double fault.
Paire, who hit a woeful 79 unforced errors -- including 16 double faults -- this time converted.
He went 3-1 up in the decider as Nishikori continued to lack consistency, then 5-3 up with another break immediately after himself handing a break to his Japanese opponent.
Serving for the match, however, Paire dropped serve, and then did so again to allow Nishikori to lead 6-5 with his service to come.
This time, Nishikori delivered to reach the Roland Garros last eight for the third time, although his display suggests he is unlikely to progress further, with Nadal resting on his 33rd birthday on Monday.
Nishikori's win snapped an eight-match winning streak on clay for Paire, who had just won the Lyon tournament.
Paire admitted he had lost concentration in the finale.
"When I won the fourth set whereas I should have lost it, and I am leading 4-1 in the fifth set, it starts turning my head and I start thinking about the next round. You're close to victory, it's not what you're supposed to do," he said.
"It's not my fault; everyone does that. I can say to myself, don't think about it, you still think about it. I serve at 5-3 and it's complicated to serve for the match."
(Reporting by Julien Pretot; Editing by Tony Lawrence and Clare Fallon)
