Kirilenko, ranked 14th and seeded second, said she hurt her back in practice and aggravated it in her opening match, which lasted only two games, against South Korean wild card Lee So-ra.
Kirilenko won her fifth and last WTA title here four years ago.
Third-seeded Kaia Kanepi of Estonia beat Galina Voskoboeva of Kazakhstan 6-2, 6-2, to reach the quarterfinals in her first tournament since the French Open.
Kanepi was coming back from a bilateral Achilles injury.
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.