The Lebanese militia group Hezbollah, fighting on the side of Syrian government forces, also had sustained heavy casualties, the New York Times reported.
At least 23 Hezbollah fighters have died in clashes in Qusayr, the opposition watchdog group Syrian Observatory for Human Rights reported.
Rebels claimed to have destroyed seven armored vehicles and killed dozens of government and Hezbollah fighters.
The Observatory said at least six rebels have been killed, admitting the total could be higher because not all bodies have been recovered.
The opposition Syrian National Coalition warned of an "impending massacre" and called for an emergency Arab League session after the Syrian and Hezbollah fighters pushed into parts of the western Syrian city of Qusayr, the hub of an important supply route for rebels fighting Syrian regime forces in Homs province, rebel forces said.
Pro-regime news agencies reported intense fighting Sunday in the city of 60,000 residents nine miles northeast of Lebanon.
The regime said its troops had fought their way to the city's center. Syrian army officers told state TV the rebel flag was brought down from Qusayr's municipal office building and the Syrian flag was hoisted in its place.
The rebels denied the extent of the regime forces' takeover of the largely Sunni Muslim city.
By day's end Sunday about 60 percent of the city, including the municipal building, was under the army's control for the first time in months, an activist told The New York Times.
At least 52 people were killed and hundreds were wounded, the British-based Observatory said. All but four of them were rebel fighters.
Residents said rebels kept fighting into the night, killing a number of Hezbollah and regime fighters.
Syrian state TV said the army had "tightened the noose on the terrorists," the regime's term for armed opponents, by attacking from several directions.
The Sunday battle -- which the opposition Local Coordination Committees of Syria said included "unprecedented shelling" from warplanes -- followed a regime offensive that began last month to capture all the villages around Qusayr so it could tighten its siege of the city and ultimately launch the Qusayr attack, which began late Saturday night with airstrikes and a barrage of artillery and rocket fire.
The battle has made Hezbollah, which recently acknowledged its military role in Syria more openly, a clear player in the 2-year-old war, the Times said.
The war increasingly pits Shiite Islamic Hezbollah, supported by Shiite-led Iran, the chief backer of Syrian President Bashar Assad, against Sunni Muslim states and their Western allies, who support the uprising, the Times said.
Hezbollah depends on Assad for its shipments of weapons from Iran.
Hezbollah is both Lebanon's most powerful political party and a militant group regarded as a resistance movement throughout much of the Arab and Muslim worlds but as a terrorist organization by the United States, Israel and six other countries.
Syrian rebels shelled Hezbollah-controlled areas Sunday, hitting the Shiite Lebanese town of Hermel in the Bekaa Valley with BM-21 Grad rockets, activists said.