Bouchard had her thigh taped during Wednesday's win over Patricia Mayr-Achleitner, and said the injury worsened overnight.
"I woke up this morning and it was much, much worse," she said. "It's hard for me to keep playing and keep making it worse."
The sixth-ranked Bouchard is enjoying a breakthrough season in which she won her maiden WTA title in Nuremberg in May, reached the final at Wimbledon and the semifinals at the Australian and French Opens.
Bouchard said she didn't want to put her participation in the WTA Finals in Singapore at risk.
"The plan is to take a lot of days off right now and really rest," she said. "The goal is to try play Singapore in a week and a half. I won't have ideal training probably but I'll give it my best."
Bouchard is the second key player to withdraw from Linz, one day after second-seeded and two-time former champion Ana Ivanovic pulled out with left hip injury.
Bouchard's departure advanced Tsvetana Pironkova of Bulgaria from the second round.
Karolina Pliskova of the Czech Republic, the only seeded player left, reached her fifth quarterfinal in three months by defeating Mona Barthel of Germany 6-4, 6-2.
The 30th-ranked Pliskova missed three match points at 5-1 but converted her next chance on serve to set up a quarterfinal against Madison Brengle of the United States, who advanced without playing after Ivanovic's withdrawal.
Barthel's defeat left Anna-Lena Friedsam as the sole German player out of five starters to reach the quarterfinals.
Friedsam made the last eight of a WTA event for the first time by routing Jana Cepelova of Slovakia 6-0, 6-4.
Friedsam didn't face a break point until serving for the match at 5-3. She lost the game before adding another break in the next to close out the win. Her next opponent is Stefanie Voegele of Switzerland.
Karin Knapp of Italy moved on when her opponent Magdalena Rybarikova of Slovakia retired after the opening set with a left leg injury. After losing the set 6-3, Rybarikova asked for medical treatment but decided to quit the match after briefly speaking to the trainer.Suggest a correction