"The Israeli enemy carried out airstrikes from the north of the occupied Palestinian territories targeting sites near Damascus," the ministry said in a statement, adding that a soldier was injured during the rare daytime attack.
Israel, which rarely comments on individual strikes but has acknowledged carrying out hundreds, usually launches airstrikes on Syria overnight.
An AFP correspondent in Damascus heard loud noises as rockets fell near the capital.
The Syrian Observatory for Human Rights said the Israeli strikes targeted sites in the Dimas area of the Damascus countryside, where Iran-backed groups and the Syrian regime's military operate.
An Israeli strike on Friday targeted Syrian regime military sites near Damascus International Airport and in the southern countryside of the capital, according to the UK-based war monitor.
In September, five soldiers were killed in an Israeli strike around Damascus, and Israeli airstrikes in June put Damascus airport out of service for nearly two weeks.
Since the civil war erupted in Syria in 2011, Israel has carried out hundreds of strikes against its northern neighbour, targeting regime troops as well as allied Iran-backed forces and Hezbollah fighters.
Israel has said its air campaign is necessary to stop arch-foe Iran from gaining a foothold on its doorstep.
Syria's ongoing conflict, which erupted after the brutal repression of anti-government protests, has killed nearly half a million people and forced around half of the country's pre-war population from their homes.