The incident took place on Market Lane yesterday.
One boy was found in posession of a baton-style weapon and screwdrivers and was arrested.
A post on Winchester Police's Facebook page read: "Winchester City Police attended Middlebrook St today and detained two juveniles who were earlier captured on CCTV jumping up and down on top of a Police car in broad daylight in Market Lane.
"One of these males was found in possession of a Police baton type weapon and screwdrivers, he has been arrested.
"Please report any anti social behaviour to Police via 101 or online #CrimeStoppers #Zerotolerance."