Senior Superintendent of Police Syed Pir M Shah said that investigations had revealed that youngsters Danish and Ali were killed when a police party opened fire on them in Bahadurabad area late last night.
"Initially the impression given was that the two had fallen victim to target killers," he said.
Police claim that the victims, along with four others on three bikes, refused to stop at a police checkpoint near the Tipu Sultan signal.
The police opened fire and both were killed on the spot.
Earlier this week, the brutal murder of 46 members of the Shia Ismaili community prompted the civilian and military leadership into expanding operations to rid violence-prone Karachi of crime and terror.