The 14th-ranked Kirilenko said she hurt her back in practice and aggravated it in in the two games played against South Korean wild-card Lee So-ra.
Kirilenko won her fifth and last WTA title here four years ago.
Third-seeded Kaia Kanepi, returning from an Achilles injury, beat Galina Voskoboeva 6-2, 6-2 to reach the quarterfinals in her first tournament since the French Open.
Kiki Bertens of the Netherlands made her first appearance in the last eight since she won her first title in April in Fez, Morocco, overcoming Silvia Soler-Espinosa of Spain 1-6, 7-6 (3), 6-2.
First-round winners included No. 4 Nadia Petrova of Russia, Tamira Paszek of Austria, and Maria Jose Martinez Sanchez of Spain.