The two were shot on a busy road in the centre of Karachi, Pakistan's largest city and financial hub. The killings follow an attack that killed four soldiers last month.
No soldier had been killed in Karachi before that since March, underlining their protected status in a city where murders of policemen, politicians and prominent businessmen are common.
"The two were sitting in their official vehicle, when two men shot them from behind and fled," senior police officer Jamil Ahmed told media, Reuters reported.
Pakistan's military said unidentified gunmen riding a motorcycle fired on the soldiers.
Karachi, a metropolis of about 20 million people, is home to the stock exchange and central bank and is plagued by political, ethnic and sectarian violence.
Security officials say many politicians in the city have links to violent gangs, operating like a mafia to maintain their hold on power.
Two years ago, the military launched a crackdown targeting suspected militants and violent criminals.
Murders have sharply declined since the crackdown began, although violence is still common. In recent months, the crackdown has expanded to include alleged corruption.
Opposition politicians say the military is using it as an excuse to target them. The military denies the accusations.