French Open champion Henin-Hardenne was leading 7-6, 0-1 when she injured her left wrist in a fall, and though she played on to 0-3 she decided to withdraw as a precaution.
The result gave Clijsters, beaten by Henin-Hardenne in the Paris final this month, her fourth title of 2003 and ended her opponent's 15-match winning streak.
Clijsters is seeded number two at Wimbledon, with Henin-Hardenne at No. 3.
