The players exchanged breaks in the first two games of the match before the 26-year-old Zvonareva gained the upper hand with another break in the fifth game.
Kanepi, who knocked fourth seed Jelena Jankovic out in the third round, saved three more break points in her next service game and three more in the ninth before netting a backhand to give Zvonareva the opening set.
Zvonareva was still unable to fully take command of the match however, the second set starting with four consecutive breaks of serve before the Wimbledon finalist was pegged back after taking a 4-2 lead.
But a touch of class from Zvonareva eventually helped her close out the match, a superb lob taking her to within two points of victory and two backhand errors from Kanepi sealing the 25-year-old's fate.
"It was very tough out there for both of us," Zvonareva said. "We tried to show our best and sometimes we had some ridiculous rallies but I was putting all the effort into trying to hang in there no matter what the conditions and I'm really happy the way I pulled it out.
"In these conditions the most important thing is to find the right balance between being aggressive and being patient, between keeping the ball in play and going for your shots. I think I was able to find that balance."
The other semi-final will pit defending champion Kim Clijsters of Belgium, the second seed, against third-seeded American Venus Williams.
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