In a telephone call, Putin urged Netanyahu "to abstain from any action that could further destabilize the situation in the country, which would represent a threat to its security", the Kremlin said in a statement.
"The Syrian issue was discussed, including the recent missile strikes on the T-4 airfield in Homs by the Israeli Air Force", the report said. The attack left 14 people dead, including seven Iranian soldiers.
Trump's warning comes just days after a deadly chemical weapon attack on the outskirts of Damascus killed upwards of 60 civilians.
"The Prime Minister reiterated that Israel will not allow Iran to establish a military presence in Syria", the statement said without noting who initiated the call.
Trump took to Twitter on Wednesday to taunt Putin, saying: "Russia vows to shoot down any and all missiles fired at Syria". Also involved is Hezbollah, the Lebanese militia that launched a war against Israel in 2006 and is behind terrorist attacks across the globe.
Israel is believed to have carried out numerous raids inside Syria since 2013.
But the United States president tweeted a little bit later today saying "our relationship with Russian Federation is worse now than it has ever been, and that includes the Cold War".
He said: "On April 7, probably the last attempt to stage a chemical weapons attack in Eastern Ghouta was made".