The American, who won her 18th grand slam singles title at the U.S. Open last month, also withdrew from last week's Wuhan Open in China because of illness.
The 33-year-old had reached the last eight on the Beijing hard courts after a 6-1 1-6 6-2 win over Czech Lucie Safarova late on Thursday.
No details about the severity of the injury were revealed.
The WTA will be hopeful their star attraction will be fit to defend her WTA Finals title in Singapore later this month after recently losing headline act, China's Li Na, to retirement.
Unseeded Stosur will face either Wimbledon champion Petra Kvitova, who reached the last eight after Serena's sister Venus pulled out of their third round match with a viral illness, or Italian Roberta Vinci in the last four.
