The statement by Netanyahu comes just days after Israel purportedly carried out an airstrike against a Syrian military base where Iran is also operating.
The Israeli leader, who has often said that Iran and its pursuit of nuclear weapons is an existential threat to Israel, said that recent events "teach us that standing up to evil and aggression is the mission imposed on every generation".
While Russia, Iran and Syria have accused Israel of carrying out the pre-dawn attack, Tel Aviv has refused to comment.
Russian President Vladimir Putin and Prime Minister Benjamin Netanyahu spoke on Wednesday, and the Russian leader urged Israel not to take action in Syria and to threaten its security.
In its statement on the conversation, Netanyahu's office said: "The prime minister reiterated that Israel will not allow Iran to establish a military presence in Syria".
The attack left 14 people dead, including seven Iranian soldiers.
Israel has struck Syrian positions dozens of times since the start of the war six years ago.
On Tuesday, an Iranian official said the airstrike would "not remain without a response", according to Lebanese news channel Al Mayadeen.
Russian Federation intervened in Syria's war in 2015, helping tip the war in Assad's favour.
Russian Federation on Wednesday also threatened to shoot down any possible USA missiles fired into Syria, as worldwide powers considered a unified response to a deadly chemical attack in the war-torn country, which the White House said Syria and Russian Federation were responsible for.