The world number two conceded her fourth-round match to Marion Bartoli 3-6 3-1, largely as a precaution with Fed Cup duties and the clay court season fast approaching.
Bartoli, the 15th seed, advances to the quarter-finals where she will face 19th-seeded Ana Ivanovic, a 6-4 6-2 winner against fellow Serb and defending champion Jelena Jankovic earlier on Tuesday.
Although Clijsters had won the opening set on the hard-court surface, she summoned her trainer for treatment on her shoulder when trailing 1-2 in the second and withdrew one game later.
"It's not that I'm really, really worried about it, but it is something that I have to pay attention to and that I don't want to risk," the 27-year-old Belgian, champion here in 2003 and 2005, told reporters.
"Can I take painkillers for it and not feel it during a match? Yes, I think so but I don't want to risk tearing it. I don't want to be... taking medication to cover the pain, not knowing if it's getting worse during my match."
The Belgian said her shoulder pain was mainly affected by serving and trying to hit high forehands.
"A couple of times today when she wrong-footed me and I went out for my backhand where I tried to do this, I could just feel it in the back," Clijsters added.
(flandersnews and reuters)