The assault on Mufti Jamil and Nazir Ahmad Taunsvi happened on Saturday in the centre of Karachi, said deputy police chief in Karachi, Fayaz Lighari.
"They had both already died when they arrived here," said Dr Asif Khukhar at Karachi's Civil Hospital.
The attack comes amid fears of escalating sectarian violence in Pakistan, following two bombings against religious targets this month, killing more than 70 people.
Both Jamil and Taunsvi were close associates of another Sunni cleric, Mufti Nizam al-Din Shamzai, whose shooting death in Karachi in May sparked riots by followers in the city.
There was no immediate word on who was behind the assault, but suspicion would likely fall on minority Shia fighters.
Pakistan has a history of sectarian violence. While most majority Sunnis and Shia live together peacefully, small armed groups from both sects have staged attacks.
Forty Sunni Muslims were killed
by a car bombing on 7 October
The first of the two attacks this month targeted a Shia mosque, killing 31 people in the eastern city of Sialkot on 1 October. Six days later, a car bombing at a gathering of Sunni followers in the central city of Multan killed 40 people.
No group claimed responsibility for the attacks, which prompted authorities to ban religious and political gatherings across the country - except for Friday prayers at mosques.