The Israeli military claimed the aircraft targeted "a terror site located between Beirut and Sidon in response" to the attack.
It was the first air strike on the area since the 2006 war.
Ramez Mustafa, a Lebanon-based official with the Popular Front for the Liberation of Palestine-General Command, said the warplanes had struck their base in Naameh, 10 miles south of Beirut.
The PFLP-GC is known for ties with the Syrian government, but Mr Mustapha denied any link between his fighters and the rockets fired at Israel.
The Abdullah Azzam Brigades, an al-Qaida-inspired group based in Lebanon, has claimed responsibility for the attack.
Group spokesman Sirajuddin Zurayqat said in a tweet that fighters from the group's Ziad Jarrah Battalions had fired the rockets.
A statement by the Israeli army said: "Israel will not tolerate terrorist aggression originating from Lebanese territory."
Israeli Prime Minister Benjamin Netanyahu said: "We are acting on all fronts, in the north and in the south, to defend Israel from such attacks.
"We employ various measures, both defensive and preventive and we are acting responsibly," he claimed.
"Our policy is clear - to protect and to prevent. Whoever tries to harm us should know we will harm them."