According to the NGO Syrian Observatory for Human Rights, the strike targeted the service centre of a foundation affiliated with pro-Iranian groups including Lebanon's Hezbollah.
The strike was near Sayyida Zeinab, which is home to an important Shiite sanctuary and is defended by pro-Iranian militias and the army.
Since the beginning of the Syrian civil war in 2011, Israel has carried out hundreds of strikes in the country, mainly targeting army positions and Iran-backed fighters, including from Hezbollah.
"At around 11:40 pm, the Israeli enemy carried out an aerial assault from the occupied Syrian Golan, targeting a number of positions in the southern region, killing two people and injuring a soldier," the SANA report said.
It said Syrian air defence had also shot down some missiles, without giving further details.
The Observatory, however, said that three people were killed in the strike, including an elderly woman, with another 11 injured.
It had initially reported one death.
On June 19, a Syrian army officer was killed in the same region, according to SANA.
Israeli strikes have increased since the Palestinian militant group Hamas's October 7 attack on Israel sparked the war in the Gaza Strip.
Iran, which backs both Hamas and Hezbollah, has long been a key ally of the Syrian government, but has said repeatedly that it has no combat troops in Syria, only officers to provide military advice and training.
Israeli authorities rarely comment on the strikes, but have repeatedly said they will not allow arch-enemy Iran to expand its presence in Syria.
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