Information Minister Shaikh Rashid told journalists on Saturday the identification of Abd al-Rahman Khadar, a Canadian-born Egyptian, was established after DNA testing.
The tests were necessary as his body had been badly mutilated during the military operation.
His son was also injured in the operation but his condition is stable.
A security official declined to say whether the injured son was in US or Pakistani custody. "We don't speak on these issues," he said.
Khadar is the second from among the eight suspects killed in South Waziristan to be identified by the US and Pakistani authorities.
China's terror list
Earlier, another suspect was identified as Hasan Mahsum, who was described by China as its top "terrorist" along with 10 other ethnic Uighur Muslim separatists, all from China's western Xinjiang region.
"We don't speak on these issues [of handing suspects over to US custody]"
Pakistani security official
Mahsum was identified as a leader in the East Turkistan Islamic Movement (ETIM).
The army had also arrested 18 suspects during the operation at Angoor Ada in in South Waziristan, a rugged region with a population of around 400,000.
It has been in the spotlight as a haven for al-Qaida and Taliban fighters fleeing US military operations across the border in Afghanistan.
Two Pakistani soldiers were also killed in a gunbattle with the suspects.
The Angoor Ada skirmish was one of the fiercest waged by Pakistani troops against al-Qaida and Taliban suspects since Pakistan joined the Unites States in security operations two years ago.
Angoor Ada faces Afghanistan's Shkin district and is just 15 kilometres from the Afghan town of Barmal, part of which was reportedly controlled by Taliban.
More than 500 al-Qaida and Taliban suspects have been rounded up in Pakistan since Pakistan joined the US-led War on Terror, which led to the ouster of the Taliban government in Afghanistan in November 2001.
The majority of those arrested are now in US custody at the US Guantanamo Bay detention centre in Cuba.