The gunmen sped away after the attack, a police official said.
Hospital official Arshad Khokhar said the brigadier and the soldier were in stable condition.
It was unclear if the officer was involved in the South Waziristan offensive, which was launched in mid-October.
On October 22, armed men on a motorcycle shot and killed a brigadier and a soldier riding in an army jeep in what was believed to be the first assassination of an army officer in the capital.
Less than a week later, assailants attacked another brigadier as he was driving to a bank, but they escaped unharmed.
No group has claimed responsibility for the attacks, but suspicion fell on the Pakistani Taliban.
The Taliban has claimed responsibility for scores of attacks in Pakistan, many of them carried out by suicide bombers.
The Pakistani army has vowed to continue the South Waziristan offensive despite the increase in attacks.
|The Pakistani army began its offensive in South Waziristan on October 17 [EPA]
The army says it is now fighting bloody street-to-street battles in each of the three main Taliban strongholds in the region - Makeen, Sararogha and Ladha.
The military says hundreds of Taliban have been killed in the South Waziristan operation - including 24 in just the last day - and hundreds more have been wounded.
A Taliban spokesman disputed the army's claims earlier this week, saying the group has not lost even a dozen fighters.
Details are impossible to confirm since South Waziristan has been sealed off to outsiders since the offensive began. Journalists have only been allowed in on carefully orchestrated government trips.