An army official confirmed the incident, saying a number of people were killed and injured.
The official said: "The Yemeni authorities received information about an attack led by supporters of the rebellion against shops in Souq al-Lail in a bid to take over the petrol station and stock up on fuel.
"Security forces sought to strike the service station to prevent the rebels from seizing it."
Thousands of people have died since a three-year-old uprising by the Shia Zaidi minority resumed in January in Saada, according to various sources.
Relatives of Hussein Badr Eddin al-Huthi - a Zaidi Shia cleric killed in 2004 during a rebellion he led against the Yemeni government - continued the uprising after his death.
Hundreds were killed in an earlier rebellion which sought restoration of the Zaidi imamate, which ruled in Sanaa until a 1962 coup by republican forces.
An offshoot of Shia Islam, the Zaidis are a minority in mainly Sunni Yemen but form the majority in the north.
Yemen has accused Shia Iran of supporting some of the rebels.