The commander said hundreds of members of the Iran-backed Lebanese Shia Hezbollah militia had taken part in the fighting.
IS retains control over some areas of desert and villages nearby, and a few other pockets in both Iraq and Syria.
When ISIS first emerged as a major threat in Iraq and Syria in 2014 the militants were riding around in tanks and gathered in large formations, presenting visible targets for the coalition.
It has already carried out guerrilla operations in both Iraq and in Syria, and has continued to inspire lone militants to attack civilian targets in the West. The footage shows Hezbollah fighters posing with the group's flag as well as Syrian soldiers and allied militia posing with the national Syrian flag.
The battle for Al-Bukamal took on a potentially new dimension amid widely spread, yet unconfirmed reports suggested that the elusive ISIS chief Abu Bakr al-Baghdadi had recently fled to the town.
Syrian forces captured the provincial capital, Deir al-Zour, from IS on Friday.
On Tuesday, Bouthaina Shaaban, a senior adviser to Assad, described the USA forces aiding the SDF as illegal invaders.
Shaaban also pointed, in a television interview, to the example of Iraq, where the government retaliated against an autonomous Kurdish region after it held an independence referendum. Syrian troops then encircled the ISIS-held town of Al-Bukamal as the Popular Mobilization Forces crossed the border to join the fight to retake the jihadis final refuge in Syria, according to the pro-opposition, United Kingdom -based Syrian Observatory for Human Rights.
The victory in al-Bukamal comes hours after the army started storming the city, which was the last IS stronghold in that part of the country near the Iraqi border. "We have no orders to cross the borders", PMF spokesman Ahmed al-Asadi said.