President Dmitry Medvedev proposed in early November amending legislation on political parties to require "party leadership rotations" and to set restrictions on the number of terms in office.
Zyuganov, 64, has led the party since 1993, when he co-founded the movement after the collapse of the Soviet Union.
The communists also voted to expand the party's Central Committee to 105 members, 75 of whom are under 40.
Zyuganov said on Sunday the party leadership had been "rejuvenated" and given "balance".
Referring to national unease over the liberal market system that has caused the global credit crunch, Zyuganov told the congress: "The wind is again blowing into our sails."
He criticized the Russian leadership's policies and said communism is the only remedy for the financial crisis, which has shown that the collapse of capitalism is inevitable.
"It is increasingly obvious that socialism is not a product of propaganda, but a natural and unavoidable phase of development. The collapse of the speculative financial market is a turning point," he said.
Zyuganov also called for restoring the Soviet Union, which he said is now possible, and for renationalizing the country's mining, energy and other "strategic" sectors.