"Evidence submitted in the claim does not prove mass violations" and could not "influence or effect the results of the vote," commission member Marina Stavniychuk said, reading from the decision.
Yanukovych will now appeal Thursday's decision to the Supreme Court, said his campaign manager, Taras Chornovyl.
"We will call on our supporters, which are 15 million, not to split the state, to observe the law and not to recognize Yushchenko as a legitimate president," Chornovyl said.
Final preliminary results from Sunday's vote show opposition leader Viktor Yushchenko winning over Yanukovych with a margin of some 2.3 million votes.
Yanukovych had submitted 27 volumes of complaints to the commission, claiming at least 4.8 million people — mainly disabled and sick — were deprived of their right to vote by the election reforms passed by parliament after the fraudulent Nov. 21 runoff.
Yushchenko won 51.99 percent to Yanukovych's 44.19 percent in Sunday's court-ordered rerun of the vote, according to a final preliminary vote tally — a difference of about 2.3 million votes.
"In principle, we have the result," said Yaroslav Davydovych, head of the Central Election Commission. "I don't know who can doubt it."
Yanukovych's vow to challenge the results echoes Yushchenko's successful move following the Nov. 21 runoff. The court ruling calling for the runoff came amid widespread complaints from foreign monitors that the Nov. 21 vote was unfair; this time, monitors have said they didn't see mass violations.
Yanukovych's team has yet to file an appeal, and Davydovych said that many of the complaints they had received, purportedly from individual voters, were "printed on the same computer, with the same text, the same envelopes."
"This is on the conscience of those who do that," Davydovych said.
President Leonid Kuchma, in the runup to Sunday's vote, urged both candidates to accept the official result and not appeal. And the Council of Europe, the continent's top human rights watchdog, called on Yanukovych on Tuesday to accept defeat.
"I call on all parties to accept the verdict of the ballot box and to refrain from rhetoric which may fuel division in Ukraine," said Terry Davis, the council's secretary general.
Ukraine's east-west divide has deepened during the protracted election campaign. The Russian-speaking, heavily industrialized east backed Yanukovych, while cosmopolitan Kiev and the nationalistic west supported Yushchenko.
The bitterly fought campaign also frayed ties between the West and Russia. The Kremlin is nervous about the eastward expanding EU and NATO, and Russian President Vladimir Putin personally campaigned for Yanukovych in the first two rounds of voting in November. He also had congratulated Yanukovych after the fraud-marred second round, ignoring western complaints that the vote was rigged.
The Russian Foreign Ministry on Tuesday harshly criticized European observers in the weekend's elections in Ukraine and in Uzbekistan.
"It would be a serious exaggeration to present the opinion of Western observers about the elections in both Uzbekistan and Ukraine as truth in the latest instance," Foreign Ministry spokesman Alexander Yakovenko said in a statement.
Yushchenko, who draws much of his support from nationalist western Ukraine where anti-Russian feeling is high, has aimed to bring this sprawling nation of 48 million closer to the West, without alienating giant neighbor Russia.
Yushchenko said his first mission would be a trip to Moscow to try to improve relations.
"I must show Russia that our earlier ties were deformed, they were formed by Ukrainian [business] clans," Yushchenko was quoted as saying in an interview published Tuesday in Russia's Izvestia newspaper.
"We can and must turn this page if we are friends and are prepared to look one another in the eye."
Yushchenko said both countries needed a better working relationship.
"Russia is Ukraine's neighbor. It is better to argue twice with your wife than once with your neighbor," Yushchenko told Izvestia, adding that the two nations share Slavic roots, family links, culture and language.