The fifth-ranked Russian reached his first quarterfinal in six events, since winning a third title this season in Warsaw in July.
Davydenko will next face seventh-seeded Marat Safin of Russia, who beat Julien Benneteau of France 6-4, 0-6, 6-2.
Davydenko beat Safin in the final in 2006 for his second title in Moscow. He also won in 2004 and last season.
"I have no illusions,'' Safin said. "Judging from his today's match, he (Davydenko) plays and moves perfectly. I think I have little chances, but why not to try. I have nothing to loose.''
The defending champion won four straight games in the first set and five straight in the second to close out the match in 56 minutes.
"The score speaks for itself,'' Davydenko said. "I played confidently and controlled the match.''
Davydenko is looking for his fourth title this season.
Safin took a 5-2 lead in the decisive set and served the match out with an ace.
"It was a strange match,'' Safin said. "I should have played like I did in the first and the third set and it could have been finished in two sets. But there was something wrong with me in the second set.''
In other second-round action, eighth-seeded Janko Tipsarevic lost to Viktor Troicki 6-3, 6-4 in an all-Serbian match, and Igor Kunitsyn of Russia ousted Robby Ginepri of the United States 6-4, 6-3.
Ginepri was leading 4-2 in the first set before the Russian won four straight games. After trading breaks for 3-all in the second, Kunitsyn won three straight games.
Germany's Mischa Zverev beat Teimuraz Gabashvili of Russia 6-2, 2-6, 6-1 to advance to his fourth quarterfinal final this season.
In the women's draw, seventh-seeded Vera Zvonareva of Russia routed Daniela Hantuchova 6-1, 6-0. The Slovak scored only five points on Zvonareva's serve.
"I did not make unforced mistakes and was serving and returning well,'' Zvonareva said. "But I know that one can only have one or two such easy matches in a season.''
The ninth-ranked Zvonareva will be playing in her fifth quarterfinal in her home event. She has never advanced.
Nadia Petrova of Russia was a set and 3-2 up when Danish teenager Caroline Wozniacki retired with breathing problems.
In the quarterfinals, Petrova will face defending champion Elena Dementieva.
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