President Putin described Yasser Arafat's death as a "heavy loss for the Palestinian people" in a letter to Mahmud Abbas, acting leader of the Palestine Liberation Organization.
Mr. Putin said Mr. Arafat "devoted his whole life to the rightful cause of the Palestinian people" in the attempt to create an independent state alongside Israel.
He also praised what he called Mr. Arafat's "contribution to the strengthening of friendly relations between Russia and Palestine."
The head of the Russian Orthodox Church, Patriarch Alexis II, also praised Mr. Arafat for what he called the Palestinian leader's participation "in efforts to bring peace to the Holy Land."
Mr. Arafat maintained strong links with Moscow dating back to the 1960s when the Soviet Union began supplying the PLO with weapons and money in its fight with Israel.
The Middle East was one of many regional conflicts that were part of Cold War rivalry between Moscow and Washington.
However the close relationship with the PLO began to change in the late 1980s after former Soviet leader Mikhail Gorbachev came to power.
Relations cooled even further in 1990 when Mr. Gorbachev sided with the United States in condemning the Iraqi invasion of Kuwait, which Mr. Arafat supported.
After the Soviet collapse, Russia established ties with Israel and became part of the "quartet" along with the United States, the European Union and the United Nations in the Middle East peace process.
During the 1990s Mr. Arafat visited Moscow several times seeking Russia's support for his hopes of establishing an independent Palestinian state.
But Moscow's ability to influence events in the Middle East had weakened, especially as Russia tried to balance its strong diplomatic and economic ties to Israel with its long-standing links to the Palestinians.