Gabashvili was leading 4-2 when Nishikori called it a day due to a painful left hip flexor. He later withdrew from next week's Acapulco event.
"I tried to play, but if you're not 100 per cent, it's tough," Nishikori told reporters.
"I couldn't do anything today. It's going to take some time to recover. It's shocking this happened, especially since I've been playing well."
Second seed John Isner had to dig deep to win his second round match, recovering from a big deficit in a third-set tiebreak to beat Dudi Sela of Israel 3-6 6-1 7-6 (5).
In a match of fluctuating fortunes, American Isner had four match points in the 10th game of the third set before Sela, who is ranked 75th in the world, recovered to hold serve.
Buoyed by that escape, Sela led 5-2 in the tiebreak before Isner won the final five points of the match, closing it out with a forehand winner.
"It puts a lot of stress on me playing matches like that. It seems I always do it but I'm glad to get through," said Isner, who has a perfect 5-0 record in three-set matches this year.
"I wish I didn't have to dig so deep... I think he (Sela) may have got a little nervous (in the tiebreak)."
Seventh seed Marin Cilic of Croatia had a more easier outing, beating American Ryan Harrison 6-3 6-4.
In Thursday's late game, American Rhyne Williams outlasted Marcos Baghdatis of Cyprus 6-7 (7) 6-4 6-2.
(Reporting By Andrew Both in Cary, North Carolina; editing by Sudipto Ganguly)
