The WTA International hard-court event saw second seed Ana Ivanovic pull out on Wednesday with a hip injury, and the tournament was dealt a further blow shortly before Bouchard was due to take on Pironkova in the final singles match of the day.
Tipped as the next big talent in the sport, the Canadian was hoping to add to her one Tour title, but was forced to pull out through injury.
"I'm in pain just to walk so I can't play professional tennis," the 20-year-old explained to the crowd as she appeared on court in Austria.
Pironkova will now take on Karin Knapp in the last eight, after the Italian also benefited from a retirement.
Knapp took the first set over Magdalena Rybarikova 6-3, before the Slovak pulled out after struggling with an injury.
After Bouchard's withdrawal, the only seed left in the competition is Karolina Pliskova, who came through her match with Mona Barthel 6-4 6-2.
Barthel double faulted on nine occasions throughout the match as seventh seed Pliskova broken the German on five occasions, eventually closing out the win after Barthel had showed some fight in saving three match points.
Pliskova will now take on Madison Brengle, who benefited from Ivanovic's withdrawal, while elsewhere, German qualifier Anna-Lena Friedsam reached the last eight after seeing off Jana Cepelova 6-0 6-4.
Friedsam dominated the first set, converting all three of her break points and, although she allowed one opportunity to pass by at 5-3 up in the second, broke Cepelova to 15 in the next game to set up a quarter-final meeting with Stefanie Voegele.