The phone call came amid ongoing Washington-Moscow tensions over policy in the Middle East and Russia's attempts to meddling in US elections.
Russian news agencies reported the phone call also included discussion of the situation in Israel. Putin was meeting Monday in Moscow with Palestinian leader Mahmoud Abbas.
Tensions in the region are high after Syrian forces downed an Israeli F-16 fighter jet over the weekend. The jet was hit and went down Saturday in northern Israel after coming under "massive anti-aircraft fire" from Syrian forces, according to the Israeli army.
Both pilots ejected from the Israeli jet, and one was severely injured.
Russia has maintained a heavy presence in Syria to bolster the dictator there, Bashar al-Assad. The US has opposed Russia's presence in the country.
On Saturday, the White House released a statement declaring Israel "a staunch ally" of the United States.
"We support its right to defend itself from the Iranian-backed Syrian and militia forces in southern Syria," the statement from White House press secretary Sarah Sanders read.
"We call on Iran and its allies to cease provocative actions and work toward regional peace."
Sanders also released a statement on Sunday expressing condolences for the plane crash, which occurred minutes after takeoff from Moscow's Domodedovo airport. The crash killed 71 people.
Trump's relationship with Putin is complicated by the election meddling issue. Trump has said he believes Putin believes he is being earnest when he denies that Moscow attempted to sway the presidential contest in Trump's favor.
Congress passed a law over the summer requiring Trump to impose new sanctions on Russia for the meddling, but so far the administration has avoided putting the sanctions in place.