"A member of the Sindh provincial assembly was killed with three of his guards when gunmen on two motorcycles intercepted his car in Orangi neighbourhood and shot them with automatic weapons," police spokesman Imran Shaukat said.
It is the second shooting of an MQM provincial lawmaker in just over two years in the city, Pakistan's business centre with a population of 18 million.
Tensions rose in Karachi immediately after Thursday's shooting. Many markets closed and people rushed home to avoid any potential violent backlash.
The death of MQM lawmaker Raza Haider in an ambush in August 2010, sparked a fierce wave of ethnic and politically linked violence that killed scores of people.
Karachi last year saw its deadliest year in two decades, with around 2,000 people killed in violence linked to ethnic and political tensions, raising fears for elections due this year.