Clijsters won 17 points in a row early in the second set to pull away. She completed the victory in 58 minutes, raising her arms in triumph when Williams sailed a forehand long on match point.
Williams struggled to keep the ball in play and won only nine points in the second set, when Clijsters went on her roll to take a 4-love lead.
After retiring in 2007, Clijsters married and became a mother before returning to the tour last August. The title is her third since her comeback.
Clijsters will climb to 10th next week, the highest ranking for the former No. 1 since she returned to the tour.