Syrians awaiting them waved flags as the troops crossed the border, The Associated Press reported. Earlier Tuesday, a formal ceremony marked the withdrawal in the Bekaa Valley.
About 400 Syrian and Lebanese forces assembled on the narrow parade grounds and were jointly reviewed by the chiefs of staff for each as dignitaries looked on.
The Syrian army Chief of Staff, Gen. Ali Habib, defended his country's nearly three decade stay, saying Lebanon was being left a stronger nation.
"It goes without saying that Syrian armed forces didn't enter Lebanon because they wanted to, but because of a call from the Lebanese government," Habib said. "Syria never had any desires or ambitions in Lebanon except to preserve it's unity."
Syrian forces controlled much of the country's affairs for 29 years, but pressure came for them to withdraw after former Lebanese prime minister Rafik Hariri was assassinated February 14 in a car bombing.
Many Lebanese people blamed Damascus for the killing, which sparked massive demonstrations calling for Syria to leave the nation.
Opposition groups also called on Lebanon's top security officials, all considered to be pro-Syrian, to resign.
On Monday, Lebanon's pro-Syrian security chief Jamil al-Sayyed quit after Syria over the weekend made its final push to jettison most remaining soldiers.
U.N. Secretary General Kofi Annan has dispatched a team to verify Syria's withdrawal.
A security council resolution adopted last September calls for the pullout of all foreign forces from Lebanon.
Syrians entered the country in 1976 as peacekeepers in the Lebanese civil war. By 1990, 40,000 Syrian troops remained.
Over the last 15 years, the number had decreased to 14,000.
Lebanese Army Commander Gen. Michel Suleiman said the nations will always be linked.
"Together comrades in arms against Israel ... a cooperative relationship in all areas together," he said. "To fend off all sectarianism and divisive forces. Our challenges are one. Our interests are one."
Key parliamentary elections are due to be held by May 29, two days before parliament's term ends.
Hariri was a key mover in getting a U.N. resolution to call on Syria to remove its troops and intelligence assets from Lebanon. Resolution 1559, passed last year, also called on Lebanon to disband guerrilla groups.
Hariri's death is at the center of an international investigation authorized by the U.N. Security Council.
A U.N. report released last month said the government of Syria "interfered" with governance in Lebanon in a heavy-handed way that was "the primary reason for the political polarization that ensued" before Hariri's death.