In the call, held on the initiative of the Israeli side, the two leaders also discussed the situation in Syria and the referendum in Iraq's Kurdistan, the Kremlin said in a statement.
Earlier on Wednesday, Iran's military chief Mohammad Baqeri discussed ways to deepen cooperation with the Syrian military during a visit to Damascus, pledging to fight Israel and Sunni insurgents.
"It is not acceptable for the Zionist regime to violate Syria anytime it wants," Baqeri said, according to the Islamic Republic News Agency.
On Tuesday, Netanyahu met with Russian Defense Minister Sergey Shoygu, who was visiting Israel. Netanyahu told the minister Israel would not allow increased Iranian influence in Syria, saying that "Iran needs to understand that."
The attack was prompted by the launch of an SA5-type missile at Israeli reconnaissance planes. While the Syrian missile did not hit its Israeli targets, the IDF said it decided to hit the battery.
The Syrian military warned of "dangerous consequences" following the rare strike, claiming that they successfuly hit an Israeli jet during the operation.
In response to the strike, Netanyahu called the incident "unacceptable" and warned that "if anyone attempts to harm us, we will harm them back."
Reuters contributed to this report
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