However, Iran has not yet commented about Israel's attack.
Reports on the casualties from the strikes vary, with the Syrian Army Command claiming three deaths and Syrian Observatory for Human Rights saying that 23 military members were killed.
It has been blamed for a series of recent strikes inside Syria that have killed Iranians, though it has not acknowledged those raids.
At least 15 people were killed in an airstrike on an Iranian weapons depot in Damascus.
According to CNN, Israel's Iron Dome, which is an aerial defense system, intercepted four Iranian rockets.
Israel said it had attacked almost all of Iran's military infrastructure including weapons storage, logistics sites and intelligence centres.
Israel's defense minister called on Syria's President Bashar Assad on Friday to rid his country of Iranian forces based there - warning their presence will only cause more trouble to the already war-ravaged country.
"We don't want an escalation, but won't let anyone attack us or build an infrastructure to attack us in the future", Lieberman said.
After Israel bombed Iranian targets in Syria, Israeli Prime Minister Netanyahu called the move an "appropriate" response to an alleged rocket attack by Iran's forces. He said Syria has the right to defend itself "against the aggressors".
Israel has stepped up its attacks on Syrian military positions in what is considered an attempt to prop up terrorist groups that have been suffering heavy losses and retreating on multiple fronts, most recently from their strongholds in Damascus suburbs. Israel, as it has typically done in similar incidents, neither confirmed nor denied a role.
"Iran has crossed a red line", he said.
Several members of parliament, on Wednesday, set the US flag and a copy of the nuclear agreement (JCPOA) on fire following Trump's historic and long-anticipated announcement that Washington was exiting the Iran nuclear deal.
Israel launched further attacks on Iran on Wednesday, responding to fire in Syria.
On Thursday, Israel's Ambassador to the UN Danny Danon demanded the United Nations Security Council condemn the missile strike and press for the withdrawal of Iranian forces from Syria.
The occupied Golan Heights is a plateau captured from Syria in 1967 by Israel in a move not recognised by the worldwide community.
He noted that in contacts with the leadership of both countries, including a meeting Wednesday between Netanyahu and Russian President Vladimir Putin in Moscow, "we underlined the necessity of avoiding any actions that might be mutually provocative".
The rising tension in Syria came just as the United States made a decision to withdraw from the 2015 nuclear deal with Iran and impose new sanctions, adding to the pressure on Tehran. Russian Federation called on both nations to resolve their differences by diplomatic means, Kremlin spokesman Dmitry Peskov said. "It means we are on a collision course".