One of the riders was stopped, but police allege he then rammed his bike into the open passenger door of the police car while a detective was getting out.
Police say the rider continued to lunge at the police car, forcing the policeman to dive back into the vehicle.
The motorcyclist then lost his balance while trying to escape and was arrested.
The other motorcyclist sped north along the wrong side of Springvale Road and remains on the run.
The arrested rider, a 43-year-old homeless man, was taken to hospital under police guard suffering unrelated minor injuries.
Police are appealing to anyone who saw the motorcyclists or may have dashcam footage of them on Peninsula Link, the Frankston Freeway or Springvale Road to contact Crime Stoppers on 1800 333 000 or at crimestoppersvic.com.au