Later at the Steffi Graf stadium top seeded 18-year-old Maria Sharapova, who will become world number one if she wins in Berlin, swept aside China's Shuai Peng 6-2, 6-1.
Clijsters failed to convert four match points before surrendering her match while leading 7-6, 5-6.
"(My leg) is inflamed now which is causing a lot of pressure around the muscles and the joints," said a pale-looking Clijsters, who was limping and appeared in pain.
The Belgian, who missed most of last season with a career-threatening wrist injury, said she was not sure exactly how the injury occurred but suspected it was the slide late in the second set, after which she had a sharp pain in her knee.
Clijsters added that she would have to wait several days for a scan to see if she had damaged any ligaments.
"Hopefully, if it shows that I haven't torn anything, I will be back for the French Open.... but if it does, well I don't even want to think about that," she said.
RESURGENT BELGIAN
Sharapova, currently the world number two, will next face Belgium's other ex-world number one, Justine Henin-Hardenne, in the quarter finals.
Henin-Hardenne struggled to beat Kveta Peschke of the Czech Republic 4-6, 6-4, 6-2.
Sharapova, who had a bye into the second round and has lost just seven games in the tournament so far, looked composed and confident on the court.
"I haven't won anything since last year. But I feel relaxed and good. I haven't had a challenge yet and I think my next match is going to be tougher," said the Russian.
Second seed and defending champion Amelie Mauresmo made a shaky start against her French compatriot Virginie Razzano, losing her first two service games, but after trailing 4-1 she found her form to win the next 10 games in succession.
Razzano broke again as Mauresmo served for the match, only for the defending champion to break back and win 6-4, 6-2.
Clijsters was treated courtside by the WTA trainer but, after failing to convert any of her match points, the four-time grand slam finalist who has leapt up the rankings from 133 last month to 17, ended her ordeal on the punishing red clay.
Former French Open winner Mary Pierce lost 6-2, 7-5 to sixth seed Nadia Petrova and a third Russian also made progress when eighth seed Elena Bovina beat Meghann Shaughnessy of the United States 6-4, 6-2.
Local favourite Julia Schruff of Germany, who played the match of her life on Wednesday when she knocked out third seed Anna Myskina of Russia, lost to 13th seed Jelena Jankovic of Serbia and Montenegro 6-3, 6-2.