The commission said more than 25 percent of the signatures Yavlinsky submitted as part of his bid were inadmissible. A candidate is disqualified if more than 5 percent of the 2 million required signatures are thrown out.
The commission's decision confirmed information leaked earlier this week that Yavlinsky would be removed from the race.
Yavlinsky can file an appeal of the commission's decision with the Supreme Court within 10 days, commission secretary Nikolai Konkin said, RIA-Novosti reported.
Yavlinsky tweeted Thursday that he had received the official report from the commission regarding his bid, which said less than 3 percent of the disqualified signature forms contained improper signatures, while around 23 percent of the forms were thrown out for "other violations".
Konkin said Friday that photocopied signature forms had been included in Yavlinsky's bid.