A Ministry of Defence spokesman said the aircraft had gone out of contact, sparking the incident.
The plane was reported to have been en route from France to Mexico, via Iceland.
It is thought it was being delivered from Airbus for the Mexican airline Volaris, and is understood not to have had any passengers on board.
An RAF spokesman said: “Quick reaction alert Typhoon aircraft were launched today from RAF Coningsby and RAF Lossiemouth to identify an unresponsive civilian aircraft.
"The Typhoon aircraft were authorised to transit at supersonic speed for operational reasons.
"Any inconvenience caused to local residents is regretted.
"Communications were re-established and the aircraft has been safely escorted by the Lossiemouth aircraft to Prestwick airport.”
Police Scotland said the aircraft was diverted to Prestwick at about 2:40pm and landed safely at 3:57pm.
It said: "A full emergency response has been put into action at the airport.
"Emergency services are in attendance to establish the full circumstances."
A Prestwick Airport spokeswoman said: “We can confirm an aircraft has been diverted to the airport following a temporary loss of communications.
"Some roads surrounding the airport have been closed as a precautionary measure.