"I consider the mission set for the defence ministry and the armed forces on the whole has been accomplished. 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," Putin said at the Kremlin.
The pullout of the Russian forces will be a huge blow to Assad, whose regime was tottering at the brink of a collapse when Putin sent troops to Syrian ground six months back.
However, Damascus denied there was any rift with the Kremlin, its staunchest ally. President Assad had agreed on the reduction of forces in a telephone call with Putin, his office said.
Assad's office also underscored that President Putin offered to continue his support for Syria in "confronting terrorism."
The partial pullout was "in accordance with the situation on the ground", Assad's office said in a statement.
"The whole subject happened in complete coordination between the Russian and Syrian sides, and is a step that was carefully and accurately studied for some time," the statement added.
A Kremlin spokesman said Putin and Assad spoke on phone before the pullout was announced but that they did not discuss Assad's future in the aftermath of a political end to the violence.
The surprise move by Putin even baffled the leaders of the anti-Assad coalition. "Nobody knows what is in Putin's mind," an opposition spokesman said, according to Reuters.