Aljazeera's correspondent in Lebanon said the Syrian army's intelligence chief in Lebanon, Major-General Rustum Ghazala, crossed the border and arrived in Damascus on Monday.
Ghazala's departure came after Lebanese security forces took control of the last positions vacated by Syrian forces in Anjar.
The final handover of control to Lebanese forces will be carried out on Tuesday in a ceremony where Syrian forces will be honoured for their services to Lebanon.
Earlier, on Sunday, Syrian soldiers were seen loading ammunition and knocking down the walls of an old base in eastern Lebanon, effectively ending a 29-year military presence.
Under pouring rain, a convoy of 200 armoured vehicles towing cannons and rocket launchers, T-52 and T72 tanks, military trucks and buses carrying more than 500 soldiers were seen heading to the Masnaa border point.
Most of the last 1000 Syrian troops in Lebanon have withdrawn in the past few days. A senior Lebanese military officer said 300 would remain behind until Tuesday for the final ceremony.
"All Syrian troops will leave Lebanon by Tuesday," an officer said, speaking on condition of anonymity.
By meeting international demands to pull out all its troops from Lebanon, Syria hopes to patch up its troubled relations with the West but the end to a lengthy deployment risks delivering a serious blow to the government's authority, analysts say.
"A humbling exit that could have been so different," was how one dissident academic, political scientist Michel Kilo, described the withdrawal.
"A humbling exit that could have been so different"
Syrian political scientist
He recalled how Syria had repeatedly declined to withdraw its troops when it had the opportunity to do so of its own free will.
By failing to withdraw after Israel's 2000 pullout from the south, Damascus missed the chance of a hero's send-off.
Now the government needed to accept the "sea change" in the politics of its smaller neighbour and undertake not just a troop withdrawal but a "complete disengagement" from Lebanon, Kilo said.