A crane removes a burnt Israeli Humvee from a street in the southern Syrian village of Beit Jin. AFP
"It is very important that Israel maintain a strong and true dialogue with Syria, and that nothing takes place that will interfere with Syria's evolution into a prosperous State," Trump said on his Truth Social platform.
The US leader has been pushing for a security pact between Israel and Syria since President Ahmed al-Sharaa's Islamist coalition overthrew longtime ruler Bashar al-Assad a year ago.
But tensions have risen over hundreds of strikes by Israel on Syria, and in the deadliest so far, Israeli forces killed 13 people on Friday in an operation in the southern village of Beit Jin.
Syria called the Israeli operation a "war crime." Israel said it targeted an Islamist group.
Trump said he was "very satisfied" with Syria's performance under former Islamist rebel Sharaa, who made a historic visit to the White House a few weeks ago.
The US president insisted that Sharaa "is working diligently to make sure good things happen, and that both Syria and Israel will have a long and prosperous relationship together."
He added that the United States was "doing everything within our power to make sure the Government of Syria continues to do what was intended" to rebuild the war-torn country.
Good relations between Syria and Israel would add to his efforts for a wider Middle East peace following the fragile Gaza ceasefire in October, added Trump.
The Trump administration lifted sanctions against Syria as part of its efforts to help Sharaa, while Washington says Damascus is joining the global coalition against the Islamic State group.
Trump spoke to Israeli Prime Minister Benjamin Netanyahu and invited him for another White House visit, Netanyahu's office said shortly after Trump issued the warning.
The Israeli occupation army said the targets of the Beit Jin operation were fighters from Jamaa Islamiya, an Islamist group based in Lebanon.
Netanyahu, meanwhile, drew a sharp rebuke from Damascus and others in the region after visiting Israeli troops deployed in the buffer zone, which has separated Israeli and Syrian forces on the Golan Heights since 1974.
Short link: