The US-led coalition said in a statement that an F-15E Strike Eagle jet destroyed the Shaheed-129 drone around 12:30 am (2130 GMT) northeast of the Al-Tanaf garrison, which is close to the Jordanian border.
"It displayed hostile intent and advanced on coalition forces," the statement read.
Coalition troops were working in the area alongside local forces who are being trained to fight the so-called Islamic State group.
A US military official told AFP the drone was "on a run toward our folks to drop a munition on them," so the coalition shot the unmanned aircraft down in self defence.
Coalition forces use the area - just northeast of the Jordanian border - as a training and staging area for attacks against IS.
The incident has similar hallmarks to a June 8 shoot- down, when a US F-15 destroyed a pro-regime drone after it dropped what turned out to be a dud bomb near US-backed local forces.
It also comes after an American F/A-18E Super Hornet fighter jet shot down a Syrian SU-22 fighter-bomber Sunday in northern Syria as it "dropped bombs" near the Syrian Democratic Forces, a US-backed alliance fighting IS.
The downing of the regime jet led Moscow to say it would sever a vital hotline it uses to communicate with the US coalition to avoid mishaps in Syria's increasingly crowded and complicated battlespace.
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