By Peter Simpson
Australian Stosur, the sixth seed and world number seven, was beaten 7-5 1-6 7-5 by Kirilenko, who defeated her at the same stage of last week's Pan Pacific Open in Tokyo.
"I didn't get off to as good a start as you want going into a third set," said Stosur. "Three love down and then 5-2 down - that's not a deficit you want to be in when it's the last set of the match.
"I've only played two tournaments since winning the U.S. Open, so I don't think it's the end of the world with the two results that I've had," she added.
Defending champion Caroline Wozniacki reached the Beijing third round with a text-book 6-2 6-3 win over Australian Jarmila Gajdosova.
The Danish world number one, who had struggled in her first round, was rarely troubled by the big-hitting, 34th-ranked Gajdosova.
Men's first seed Jo-Wilfried Tsonga smashed his way to the second round, beating Bulgarian Grigor Dimitrov 7-6 7-5.
"Of course I think I have chance, but it's tough for me to say how much," said Tsonga.
The showcase WTA women's and ATP men's tournament at the National Tennis Center in the Chinese capital have suffered a bout of shock exits and injury pull outs.
Men's world number one and defending champion Novak Djokovic also withdrew with a back complaint.
(Editing by Clare Fallon)