The provincial leader, identified as Maulana Muhammad Qasim, was also the Khateeb of Jamia Masjid Noorani. It had earlier been reported that Qasim was the provincial chief.
He was on his was to lead Friday prayers when he was targeted by unidentified assailants on motorbikes.
Markets in the area were shut down after the incident and protestors burnt tyres on the road.
More than three prayer leaders have been targeted in Quetta in the last five months.
Earlier, two people had been shot dead after assailants barged into a medical store and shoe shop on Mecangi road and opened fire on the victims.
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