Former No. 1 Sharapova served to go up 6-5 in the final set and then broke Benesova to close out the match in 1 hour, 39 minutes and set up a semifinal with either Magdalena Rybarikova or Agnieska Radwanska who play later on Thursday.
Sharapova has struggled since returning from a 10-month injury layoff but said after Wednesday's win she is starting to feel more comfortable on the court.
"I feel like I'm starting to get the feeling back of being able to figure things out automatically," Sharapova said. "Like knowing when you have to be patient and when you have to be aggressive."
Sharapova won her first tournament as a professional at the Japan Open in 2003 and won in Tokyo in 2005. With the top six seeds all out of the tournament, she is positioned well for another shot at a title in the $2 million tournament at Ariake Colosseum.
Sharapova had eight double faults and six aces in the match against Benesova but said she can live with that balance in her service game.
"The goal is to be aggressive," Sharapova said. "I can make a few more errors but it's all about execution and knowing when not to make a mistake."
Earlier, Jelena Jankovic of Serbia advanced to the semifinals with a 6-4, 6-3 win over Marion Bartoli.
Jankovic, the tournament's seventh-seeded player, posted her first win over Bartoli this season after struggling against the 14th-seeded Frenchwoman in previous matches.
"When my thoughts are on the court, I play at another level," Jankovic said. "That wasn't the case in previous matches. Today, I controlled the match and didn't let her play her game."
Jankovic has lost to Bartoli twice this year, at the Australian Open and at Stanford. The former No. 1 said she is much more focused now that some personal problems are behind her.
"A lot of things happened this year," Jankovic said. "My mother had surgery and my grandmother died, and that affects your game. Tennis becomes secondary because there are more important things in life than tennis, but now it's the end of the year and hopefully I can finish strong and make a good start to 2010."
Jankovic is the highest seeded player left in the tournament.
Top-ranked Dinara Safina of Russia, Venus Williams and French Open champion Svetlana Kuznetsova all lost their opening matches Monday after first-round byes.