The Saudi diplomat, identified in media reports as Hasan M M Al-Kahtani, was attacked by four gunmen riding two motorcycles while he was driving to work.
The attack occurred a short distance from the Bahrain consulate. The Saudi Embassy in Islamabad confirmed that the victim was a diplomat.
Police officials said the gunmen intercepted the car and fired over a dozen bullets at the victim. He was declared dead on arrival at the Jinnah Hospital.
No group claimed responsibility for the attack. On May 11, two men riding a motorcycle lobbed two low intensity explosive devices at the Saudi consulate in Karachi though no one was injured in the attack.
Saudi officials said the blasts caused minor damage to buildings within the consulate compound.
The attacks came in the wake of the May 2 raid by US special forces in the garrison city of Abbottabad that killed al-Qaeda leader Osama bin Laden.
Saudi Assistant Foreign Minister Prince Khaled bin Saud had urged Pakistani authorities to ensure the protection of the kingdom's diplomatic missions in the country.