Bilal Shaikh and two other aides died in the blast, which took place near an office of Mr Zardari's Pakistan People's Party (PPP).
Several more people are reported to have been wounded in the explosion.
An active member of the PPP, Mr Sheikh was responsible for the safety of Mr Zardari's son, Bilawal Bhutto Zardari.
Mr Sheikh had survived an assassination attempt near his home in Karachi about a year ago.
The president's residence is also in the city, which has been plagued by violent turf wars between rival political groups and heavily armed gangs linked to them.
Authorities said initial investigations showed it was a suicide attack.
Security forces cordoned off the area in the Guru Mandir neighbourhood in central Karachi, following Wednesday's bombing.
A police escort was accompanying Mr Sheikh's white armoured car when the attack took place.
Officials said the bomber was thought to have followed the vehicles and detonated the explosives when the security chief stopped to get out of his car.
"It seems that the suicide attacker walked up to Sheikh's vehicle and blew himself up outside the front passenger seat of the vehicle where Sheikh was seated," police officer Raja Umar Khattab said.
No group has said it was behind the bombing.
There has been a series of attacks blamed on Islamist groups, including the Pakistan Taliban, around the country since the new Prime Minister Nawaz Sharif was sworn in last month.
Mr Sharif, who has pledged new action on terrorism, is under mounting pressure to explain how he intends stopping the bloodshed, observers say.
The chief security officer of Pakistani President Asif Ali Zardari has been killed in a bomb attack in the port city of Karachi, police say.