The air raids on Sunday night came less than 24 hours after commandos stormed an office building and rescued dozens of security officials taken captive after an attack on the general army headquarters in Rawalpindi.
"The jets hit and destroyed two of their hideouts in Makeen and Ladha and we have a total of about 16 militants killed," a unnamed Pakistani intelligence official told Reuters news agency.
But the military has been conducting air and artillery strikes in South Waziristan for months, while moving troops, blockading the region and trying to split armed opposition to Islamabad's authority.
However, a ground offensive has yet to begin and may prove to be the army's toughest test since fighters turned on the state.
Nevertheless, Rehman Malik, the interior minister, in an interview in Singapore said a ground offensive was "imminent".
"There is no mercy for them because our determination and resolve is to flush them out," he said.
"They have no room in Pakistan, I promise you."
Malik said members of the Pakistani Taliban and al-Qaeda were suspected to have been behind Saturday's attack on army headquarters, which ended a week when suicide bombers struck in the capital Islamabad and Peshawar, killing more than 50 people.
He also said the offensive against the fighters in South Waziristan was no longer a matter of choice.
"It is not an issue of commitment, it is becoming a compulsion because there was an appeal from the local tribes that we should do the operation," Malik said.
In an interview with Al Jazeera, Imtiaz Gul, a political analyst, said he agreed that the government was correct to commence an offensive against South Waziristan.
"A lot of al-Qaeda and ideologically tainted people belonging to the Islamic movement of Uzbekistan under the patronage of the Taliban are sheltering there," he said.
Source: Al Jazeera (English)