He said the Russian intervention had largely achieved its objectives.
The comments come amid fresh peace talks in Geneva aimed at resolving the five-year Syrian conflict.
Russia is a key ally of Syrian President Bashar al-Assad, whose office said in a statement he had agreed to the move.
The pullout was "in accordance with the situation on the ground", the statement said.
Russia began its campaign of air strikes in Syria last September, tipping the balance in favor of the Syrian government and allowing it to recapture territory from rebels.
"I consider the mission set for the defense ministry and the armed forces on the whole has been accomplished," Mr Putin said in a meeting at the Kremlin.
"I am therefore ordering the defense ministry to begin the withdrawal of the main part of our military force from the Syrian Arab Republic from tomorrow."
When Russian airstrikes began in Syria, President Assad's regime was on the brink of collapse.
Less than six months later, Russia says its action allowed Syrian government troops to retake 10,000 sq km (3,860 sq miles) of territory.
By intervening, Vladimir Putin made clear that Russia was prepared to assert its interests. The results ensure Moscow a bigger say in what happens at the peace talks.
The decision to scale down Russian operations may partly be fueled by cost, given falling oil prices; it could also be driven by a desire to end Russia's isolation and western sanctions
But whilst Vladimir Putin has ordered his foreign minister to focus efforts on the political front in Syria, he appears to be hedging his bets.
Critically, sophisticated air defense systems seem set to stay.
And as we have never been told officially how many troops were ever sent to Syria, we are unlikely to know how many will remain. Read more: