After reaching the semi-finals at the Rome Open last week, she wrapped up victory in an hour and 12 minutes.
Elsewhere Russian qualifier Vera Dushevina beat Italy's Francesca Schiavone 6-3 4-6 6-2 in an entertaining tussle.
The Magic Box arena can change shape against the surrounding landscape
Dushevina's triumph was a welcome boost for the Russian contingent on a day which saw Kuznetsova and Dementieva go out.
Kuznetsova had won nine of her 10 matches on clay coming into the Madrid Open, but her bid for a third straight final came unstuck against Bondarenko, the third time she has lost to the Ukrainian on clay.
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