He told a Kremlin meeting 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 and the Kremlin said he had been informed.
Russia's entry into the Syrian civil war in September 2015 tipped the balance in favour of the Syrian government, allowing it to recapture territory from rebels.
"I consider the mission set for the Defence Ministry and the armed forces on the whole has been accomplished," Mr Putin said at the Kremlin meeting.
"I am therefore ordering the Defence Ministry to begin the withdrawal of the main part of our military force from the Syrian Arab Republic from tomorrow."
Mr Putin also said that Russia's Hmeimim airbase and its Mediterranean port at Tartus would continue to operate as normal.
He said both must be protected "from land, air and sea".
The UN's envoy to Syria, Staffan de Mistura has meanwhile described the latest peace talks as a "moment of truth".
He said there was no "plan B" should the talks fail, with the only alternative a return to war.
A cessation of hostilities agreed by most participants in the conflict began late last month - but there have been reports of some violations on all sides.
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