The prayer was led by former City Nazim Nematullah Khan Advocate amid tight security.
A large number of JI workers, PML-N leader Saleem Zia, PPP leader Najmi Alam, ANP leader Ameer Nawab attended the funeral prayers of Pervez Mehmood.
The JI has given strike call in Karachi and a country-wide protest against the targeted killing of Mehmood on Wednesday.
The party staged sit-in outside the Chief Minister House against the murder of its leader.
Nasrullah Shajee, a local leader of the right-wing party appealed to the people of Karachi to keep close their business on Wednesday.
Another worker of JI identified Abdul Ahad was shot dead in during the protest in the city . Two people were injured in Gulistan-e-Jauher area of the metropolis.