The gunmen riding on a motorcycle opened fire on the military police vehicle while it was passing through the Tibet centre area on the congested M A Jinnah road, Deputy Inspector General (DIG) police for southern region Jamil Ahmad said.
Two security personnel who were in the car were critically injured and rushed to a hospital where they died of injuries.
Nobody took responsibility of the attack which came about two weeks after four soldiers of paramilitary Rangers were killed in a similar attack in Karachi.
Prime Minister Nawaz Sharif has condemned the firing incident.
"We would not be deterred by such cowardly terrorist attacks on our brave Jawans. Peace and stability is the future of Karachi, which is because of the national resolve against terrorists and great sacrifices made by our Jawans," said the Prime Minister.