The Japanese player, ranked 15th in the world, was trailing 1–6, 0–1 against Czech Karolina Muchova when she was forced to retire.
Osaka had taken a medical timeout in the first set.
"I want to thank everyone who came to watch the match and I apologize for not being able to finish the match," Osaka told the crowd.
The four-time Grand Slam winner has never made it past the third round at Wimbledon, but her runner-up finish at the grass-court tournament in Bad Homburg showed that there was hope for Osaka.
Naomi Osaka is seeded 14th at Wimbledon and is drawn to face Elsa Jacquemot of France in the first round.
Now her start is uncertain.
