Mr Nadezhdin has been relatively critical of Vladimir Putin’s full-scale war in Ukraine when few dissenting voices have been tolerated in Russia.
Election authorities claimed more than 15% of the signatures he submitted with his candidate application were flawed.
He had tried to challenge this, but the commission rejected his bid.
Refusing to give up, Mr Nadezhdin, 60, said on social media that he would challenge the decision in Russia’s Supreme Court.
The Central Election Commission said that of the 105,000 signatures submitted by Mr Nadezhdin, more than 9,000 were invalid. They cited a variety of violations.
That left 95,587 names, meaning he was just short of the 100,000 required signatures to register as a candidate, commission member Andrei Shutov said.
Russia’s presidential election is due to take place from 15-17 March, although the result is not in doubt as only candidates viewed as acceptable to the Kremlin are running.
A final decision on who can take part will come on Saturday, but the election commission chairwoman said it was already clear there would be four candidates on the ballot.
Other than Vladimir Putin, they include nationalist leader Leonid Slutsky, parliament deputy speaker Vladislav Davankov and Communist Nikolai Kharitonov. All their parties have broadly backed Kremlin policies and none of the trio is seen as a genuine challenger.
Trotsky’s promiscuous grandson?