An MRI scan has since revealed that the cause of Clijsters' pain was a spasm on her tensor fascia lata - a muscle on the outside of the hip.
The former world number one was leading Daniela Hantuchova 7-6 (7/4) 1-3 when she decided to call it a day.
But Clijsters remains optimistic of featuring in the year's first grand slam at Melbourne Park, which begins on January 16.
"With this one I kind of have an okay feeling," she told australianopen.com.
"If everything comes out okay it should take a little (less than) a week to get completely healed.
"I felt my left hip was getting tighter and tighter to the point I couldn't move forward with my upper body.
"The smartest choice was not to let it get any worse and try to be right for Melbourne."
The four-time grand slam champion will undergo intensive treatment over the next few days before a follow-up assessment on Wednesday.
Clijsters has had wretched luck with injuries in recent times with a foot complaint forcing her to miss last year's Wimbledon tournament and an abdominal strain ruling her out of defending her US Open crown in September.