Syrian President Bashar al-Asad met his Lebanese counterpart Emile Lahud in Damascus on Monday, and a statement later said they had agreed on the two-phase withdrawal plan.
The plan set no timetable set for a full withdrawal.
Even while al-Asad and Lahud were meeting, Syrian soldiers based in the Lebanese mountain towns of Mdairij, Soufar and Aley were dismantling communications equipment or loading personal belongings and military gear on military trucks, witnesses said.
Lebanese army soldiers in trucks waited near a Syrian military post at Dahr al-Wahsh east of Beirut as the Syrian troops prepared to leave, the witnesses said.
Al-Asad and Lahud said they respected all UN Security Council resolutions, including one demanding that Syria quit Lebanon, as well as the Taif Accord, which ended Lebanon's civil war and which envisaged a Syrian pullout from most parts of the country.
"The two sides affirmed their commitment to the Taif Accord and its mechanism"
"The two sides affirmed their commitment to the Taif Accord and its mechanism ... and their respect to all resolutions issued by the international legitimacy including Resolution 1559," their statement said.
Syria has previously said compliance with the Taif Accord amounts to fulfilling the UN resolution.
Syria has been in Lebanon since intervening in the civil war in 1976 and now has about 14,000 troops there, down from 40,000.
Damascus came under growing Lebanese, Arab and wider international pressure to withdraw its forces after the assassination last month of former Lebanese Prime Minister Rafiq al-Hariri. Syria denied accusations that it had a hand in the Beirut bombing.