According to the police, the cleric and his son were in a vehicle when unidentified gunmen opened fire on them.
Reports indicated that Madni received three bullets in his head and chest.
Maulana Madni and his second son Abdullah were attacked in 2005 as well in which Abdullah was killed while Madni received had injuries.
Madni was the Nazim of Jamia Mehmodia, which is one of the centres in the city for the proscribed organisation.
Earlier, on February 20 a leadng cleric belonging to the Barelvi sect was killed in Karachi. Forty-year-old Hafiz Adnan Sheikh Qadri was said to have had an affiliation with Dawat-e-Islami, Sunni Ittehad Council and Sunni Tehreek.
Leaders of the Sunni Tehreek had held the Sipah-e-Sahaba responsible for the killing of Qadri.
The banned SSP is known for having an active militant wing which over the last few months has been allegedly targeted by the Barelvi sect.
Two more people were killed in other incidents of target killing. In Korangi, unknown attackers broke into a house, killing a youth and injuring his father and brother.
Another man was killed in the Zaman town area of the city.
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