Clijsters had gained the first break in the match to nose ahead 2-1 and stretched it to 4-3 in the first set but from then on her game became unhinged.
The fourth seed lost her serve two more times and surrendered the set as she scooped a forehand into the net.
Despite fluffing numerous break points in the second set, Sharapova stood firm and slammed the door shut after 83 minutes by cracking a sizzling forehand down the line on match point.
"I'm going to miss it, it's been a pleasure to come here. It's always a lot of fun and I'm sorry I couldn't come up with a better match today," Clijsters said courtside with a rueful smile as the fans gave her a standing ovation.
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