The Central Reserve Police Force (CRPF) vehicle collided with a civilian car before hitting the motorcycle on Boulevard Road.
A protest broke out in the area after the accident, in which angry protesters torched the CRPF vehicle.
Police reached the spot and dispersed the protesters.
The two dead were identified as Mohammed Ashraf Hafiz, son of Mohammad Sultan Hafiz and a resident of Brain Nishat, and pedestrian Nadeem Ahmad Chapri.
A police complaint was filed, and the drivers of the CRPF vehicle and the civilian car were arrested.