State-run broadcaster Syria TV, citing a military source, said Israeli helicopters targeted three posts in Quneitra shortly before midnight (2100 GMT).
The strikes also set several fields in the area on fire, the broadcaster said.
“Earlier today, munitions were fired from Syria toward Israel,” the Israeli army, which rarely comments on strikes inside Syria, said in a tweet.
“In response, our aircraft struck military targets in southern Syria belonging to the Syrian Armed Forces.”
“We hold the Syrian regime responsible & will respond to any violation of Israeli sovereignty,” the Israel Defence Forces (IDF) continued in the tweet.
The Britain-based Syrian Observatory for Human Rights, a war monitor, said Israeli helicopters targeted a post manned by pro-Iranian militias near the village of Hadar in the countryside of Queintra.
The Observatory said that the targeted post is jointly manned by the Syrian army and pro-Iranian militias.
Earlier in the day, several powerful explosions rocked the countryside of Queintra, close to the Israeli border, a monitor reported earlier.
The Observatory said no information was available on the nature of the blasts that took place on Friday and that Syria’s ground defences had reportedly responded to “unknown targets.”
Activists in the area said Syrian government troops, positioned in rural Quneitra, had shot at a flying Israeli drone.
The Israeli military also said there were explosions on the Syrian side of the border and that one house and one civilian vehicle on the Israeli side were damaged by shrapnel.
On Monday, at least five pro-Iranian militiamen were killed in Israeli rocket attacks on the Syrian capital Damascus, the Observatory said.
Among those killed in Monday’s strikes was a member of the Iran-allied Lebanese Hezbollah movement aligned with the Syrian government.
The Israeli army said on Thursday it was reinforcing troops on its northern border as tensions rose with Hezbollah.
Iran has been a major ally of Syrian President Bashar al-Assad since a pro-democracy uprising erupted against his regime in 2011.
Israel had previously conducted strikes against targets in Syria, claiming they were part of an effort to prevent Iran from building up its military influence in the region.