All flying will be paused, though classroom studies will continue.
It comes after Defence Secretary Mark Esper ordered a review following the shooting of three sailors at a navy base by a Saudi Air Force lieutenant.
The FBI said it was trying to determine the motive of the attacker, who was shot dead by police.
Investigators say they are working on the assumption that it was an act of terrorism.
The shooting at Pensacola has placed the long-standing US-Saudi relationship under scrutiny.
Ties have already been strained by the Saudi military offensive in Yemen and the murder of Washington Post columnist Jamal Khashoggi last year.
What has the US said?
“A safety stand-down and operational pause commenced Monday for Saudi Arabian aviation students,” Navy Lt Commander Megan Isaac told the BBC.
She said the no-fly rule affects 303 Saudi students at three Florida Naval Air Stations: Pensacola, Whiting Field and Mayport.
Pentagon civilian spokesman Chuck Prichard told the BBC that the no-fly rule covered Saudi aviation students US-wide.
He said the operational pause affects 852 Saudi students enrolled in all military…