The army also regained control of the Ba’ath Party headquarters in Qusayr, killing large numbers of foreign-backed militants.
Meanwhile, the Syrian government forces have also taken full control of the Homs-Ba'albek Highway after severe clashes with militants.
Earlier in the day, the Syrian forces pounded the positions of the militants with heaviest artillery and rocket barrages.
The Syrian army has kicked off the second phase of its operation in the town after successfully concluding the first phase of battle.
The fighting for al-Qusayr, which straddles strategic supply routes important for the militants, started on Sunday after the army surrounded the area and successfully entered the town.
The command center of the al-Nusra Front has been destroyed in the battle and the army has taken control over the city center and municipality building.
Syrian soldiers, backed by volunteer fighters, are moving forward in their fight against Western-backed terrorist gangs and militant groups throughout the war-torn country.
With the government struggling with a bloody insurgency, the US, Israel and their Western allies have threatened to send more arms to militants if President Bashar al-Assad does not leave.
On Wednesday, a US Senate committee voted in favor of a bill, authorizing the government to provide foreign-sponsored militants in Syria with lethal weapons and military training.