At least 29 fighters from the Western-armed Hazm movement were killed along with six Al-Nusra Front terrorists, according to the Syrian Observatory for Human Rights.
It said fierce fighting had broken out on Friday night for Base 46, west of the city of Aleppo.
"Al-Nusra captured Base 46," said Rami Abdel Rahman, director of the Britain-based Observatory.
The offensive came a month after al-Nusra expelled Hazm from Regiment 111, another base they had taken.
Hazm is mainly present in northern Syria. Last year, it was the first to receive U.S.-made anti-tank missiles from its Western backers.
It is one of a number rebel groups that the United States classes as "moderate." They are loosely branded as the Free Syrian Army.
Meanwhile in an important gain, Syrian army takes villages in south of country.
Syrian government forces have taken control of villages in southern Syria, state media said on Saturday, part of a campaign they started this month against insurgents posing one of the biggest remaining threats to Damascus.
click to watch - Syrian army takes villages in south of country
The large offensive made swift progress and gains, made on Friday and Saturday, mark a new push in the government campaign.
Syria's state news agency SANA said the village of Tal Al-Majda in Sweida province and Tal Antar in Deraa were taken. Both are near Jordan.
The south is the last notable foothold of the mainstream rebel, non-jihadist opposition to President Bashar al-Assad, who has consolidated control over much of western Syria .
Al Qaeda's Syrian arm, the Nusra Front, is also active in the south and has clashed with western-back rebels. Rival ISIS terrorists has presence north and east of the country.
The offensive aims to shield the capital Damascus. The insurgents had made significant gains in the south in recent months, taking several military bases.