The army said pro-government forces had cleared IS fighters from the UNESCO world heritage site, where the jihadists sparked a global outcry with the systematic destruction of treasured monuments.
"Palmyra will be the central base to broaden operations... Against Daesh in numerous areas, primarily Deir Ezzor and Raqa," the armed forces said in a statement carried by state media, using an Arabic name for IS.
The northern city of Raqa is IS's main Syrian bastion and the oil-rich eastern province of Deir Ezzor is another key stronghold.
Palmyra is both an important symbolic and strategic prize for President Bashar al-Assad's forces, as it provides control of the surrounding desert extending all the way to the Iraqi border.
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At least 400 IS fighters were killed in the battle for the city, the Syrian Observatory for Human Rights said. On the government side, 188 troops and militiamen were killed.
"That's the heaviest losses that IS has sustained in a single battle since its creation" in 2013, the director of the Britain-based monitoring group, Rami Abdel Rahman, told AFP.
The Observatory said the pullout had been ordered by IS high command.
"A handful of IS fighters are refusing to leave the city and seem to want to fight on to the bitter end," Abdel Rahman said.
After the army took control of the city, sappers were defusing mines and bombs planted by IS in the ancient ruins, the source said.
Syrian state television broadcast footage from inside the famed Palmyra museum, where jagged pieces of sculptures lay blanketed in dust on the ground. A stone head of an unidentified statue lay in the centre of one room, surrounded by cracked columns.
Outside, in the city's main roundabout, a small group of army soldiers strolled through debris-covered streets under a clear sky.
IS, behind a string of attacks in the West including last week's Brussels bombings, is under growing pressure from Syrian and Iraqi military offensives to retake bastions of its self-proclaimed "caliphate".