A 34-year-old man from Kuwait and a 48-year-old man from Italy were detained after arriving from Vienna shortly after 19:00 BST on Sunday, police said.
The RAF confirmed Typhoon fighter jets from RAF Coningsby intercepted a Ryanair plane and escorted it to Stansted.
Police said inquiries were ongoing.
A Ryanair spokesman said the crew of the flight from Vienna to the Essex airport had been alerted to a "potential security threat on board".
He added: "In line with procedures, the captain informed UK authorities and continued to London Stansted, where the aircraft landed normally and taxied to a remote stand where passengers disembarked safely."
The Eastern Region Special Operations Unit said the men were detained under Schedule 7 of the Terrorism Act.