His candidacy was approved by 215 votes in favor and three against out of total 218 party delegates.
Zyuganov, 63, who will be running for the president for the third time next year, is so far the fourth officially nominated candidate.
The other three are leader of the Democratic Party of Russia Andrei Bogdanov, former prime minister Mikhail Kasyanov, who pledged to promote freedom, competition and dissolve the current parliament elected during the widely criticized polls, and outspoken ultranationalist politician Vladimir Zhirinovsky.
Chess grandmaster Garry Kasparov, recently jailed for five days following an opposition march, was one of the first to announce plans to pull out of the presidential race after failing to find a venue for his action group meeting.
The ruling United Russia party backed by three other pro-Kremlin parties announced on Monday it would put forward First Deputy Prime Minister Dmitry Medvedev to run. Given President Vladimir Putin's backing, Medvedev is seen as a front-runner.
