Waliur Rehman died when an unmanned US aircraft fired two missiles on a house in North Waziristan district, a Taliban and Al-Qaeda haven on the Afghan border, in the early hours of Wednesday.
The Tehreek-e-Taliban Pakistan (TTP) hailed Rehman as a "martyr" and vowed to avenge him, while blaming Pakistan's government for being responsible for the attack.
"Our six men including Waliur Rehman were killed in this attack," TTP spokesman Ehsanullah Ehsan told AFP, officially confirming the death of the key commander for the first time.
Analysts said the death of Rehman, who had a $5 million US government bounty on his head, would come as a serious blow to the TTP, which has waged a bloody campaign of bombings against the Pakistani state in recent years.
But Ehsan insisted the death would strengthen the militants' resolve, and said they would strike back in response.
"We will take revenge of these killings from the Pakistani government and the establishment," Ehsan told AFP. "Establishment" in Pakistan usually refers to the military and security services.
Washington had accused Rehman of organising attacks against US and NATO forces in Afghanistan and also wanted him in connection with a suicide attack on an American base in Afghanistan in 2009 that killed seven CIA agents.
The 42-year-old had been a key figure in the TTP since its inception in 2007 and was second-in-command of the national hierarchy behind Hakimullah Mehsud, as well as leading the group in South Waziristan.