Among the targets were a headquarters, a training facility and artillery batteries, the Israeli military said.
The Syrian army had “aided and abetted” the attack on a patrol near the ceasefire line on Tuesday, it added.
There has been no comment yet on the air strikes from Syria and it is not clear if there were any casualties.
The Israeli air force has conducted several aerial attacks on Syria since the uprising began three years ago.
Those air strikes are believed to have prevented the transfer of stockpiles of rockets from the Syrian government to Hezbollah, the Lebanese Shia Islamist movement that supports President Bashar al-Assad.
The choice of targets demonstrates that Israel is clearly blaming Syrian government forces, and not rebel fighters or units of Hezbollah for the attack on its patrol.
Israel has used artillery against Syrian targets on the Golan to respond in previous incidents, but its use of military aircraft on this occasion raises the incident to a more significant level.
At the start of a cabinet meeting on Wednesday, Israeli PM Benjamin Netanyahu warned that his country would act “forcefully” to defend itself against any attack.
The Golan Heights, a rocky plateau in south-western Syria, has a political and strategic significance that belies its size.
Israel seized the region from Syria in the closing stages of the 1967 Middle East War, and thwarted a Syrian attempt to retake it in 1973.
The two countries remain technically in a state of war, and UN observers are deployed to monitor a 44-mile-long demilitarized zone.
On Tuesday, the four Israeli soldiers were wounded, one of them seriously, when an explosive device was detonated as they approached the fence demarcating the demilitarized zone.
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