Haris and Haroon were taken into custody by a joint team of Police and Rangers who were patrolling the area at the time.
An army uniform and a handgun were also discovered from their vehicle and a First Information Report (FIR) was submitted against the accused over possessing arms at the Kohsar police station.
Concerned authorities are investigating the suspects.
Meanwhile, a Lal Masjid spokesman said that the FIR was an excuse to bar the boys in their efforts to pursue a case against former president Musharraf who was alleged for the murder of the Lal Masjid cleric.
He stressed that no uniform had been found from the auto and that only a weapon was there in the car and that was licensed gun.
The federal capital has been under a strict security for couple of years in the wake of terrorist activities across the country especially in Islamabad. Security forces of the country have always kept an eye on any suspicious activity in the city.