Lebanese police said a convoy of about 60 buses transporting soldiers and trucks loaded with their belongings crossed the Masnaa border post, 70 kilometres (42 miles) east of Beirut, at 5:00 am (0200 GMT).
They did not specify how many soldiers had actually returned to Syria.
But a Lebanese army officer, on condition of anonymity, told AFP the pullout of some 3,000 troops would be completed "in three or four days", depending on transportation being in place.
There were no tanks and just one large piece of artillery equipment in this first withdrawal from Lebanon since the redeployment kicked off on Tuesday, officials said.
On Wednesday, Syrian troops had for the second day continued to redeploy units from locations around Beirut. Four posts -- at Damour, Shweifat, Khaldeh and Aaramun -- were evacuated south of the capital.
Some 30 empty trucks and buses had earlier crossed into Lebanon to pick up troops and equipment.
Critics have said the Syrian redeployment was nothing more than a publicity stunt that did not live up to international demands for a complete withdrawal of foreign troops.
Lebanese Foreign Minister Mahmud Hammud has said the pullout of the remaining 15,000 Syrian troops would take place once the Arab-Israeli conflict is finally resolved and all Arab territories are free from Israeli occupation.
The operation comes 28 years after Damascus first sent in its troops to serve as a stabilisation force, a year after the outbreak of the 1975-1990 civil war in Lebanon.
The redeployment was the fifth in three years, during which the number of Syrian troops in Lebanon has decreased from a high of 35,000 at the end of the war.
In the previous redeployments Syrian troops were totally evacuated from Beirut and parts of the northern and Mount Lebanon areas.
The largest number of Syrian troops are deployed in the Bekaa Valley in the east of the country, near the common border.
France and the United States sponsored UN Security Council Resolution 1559, adopted on September 2 (eds: correct), that called for the complete withdrawal of foreign forces from Lebanon and respect for its sovereignty.
UN Secretary General Kofi Annan is expected to report next month on compliance with the resolution, which also demanded the disarming of militias in Lebanon.
On Wednesday, US Secretary of State Colin Powell told reporters after talks in New York with Syrian Foreign Minister Faruq al-Shara that the redeployment was a "positive" development.
"We've noted the redeployment of some Syrian troops," he said. "I think this is a positive step and we took note of it, but, of course, the resolution ... calls on the Syrians to do more and we had a good discussion of that."