In a televised address, US President Joe Biden said that he hoped Zawahiri's death would bring "closure" to families of the 3,000 people killed in the United States on 9/11.
He said that there were no civilian casualties in the operation that was conducted over the weekend. "Justice has been delivered, and this terrorist leader is no more", the US president said.
"The United States continues to demonstrate our resolve and our capacity to defend the American people against those who seek to do us harm. Tonight we made clear: No matter how long it takes. No matter where you try to hide. We will find you," he later tweeted.
The Federal Bureau of Investigation (FBI) has added a "deceased" caption under the profile image of Al Qaeda chief Ayman al-Zawahiri on its website.
Officials said Zawahiri was on the balcony of his Kabul residence when he was targeted with two Hellfire missiles on July 31, adding that President Biden gave his go-ahead to the operation on July 25.
Apparent photographs of the building show windows blown out on one floor, but the rest of the building appeared completely intact. Members of Zawahiri's family were present at the home, but "were purposely not targeted and were not harmed," officials said.
US officials called Zawahiri's presence in the Afghan capital Kabul a "clear violation" of a deal the Taliban had signed with the US in Doha in 2020 that paved the way for the US withdrawal from Afghanistan.
Under the 2020 Doha deal, the Taliban promised not to allow Afghanistan to be used again as a launchpad for terrorism, but experts believe the group never broke their ties with Al-Qaeda.
In a statement, Taliban spokesman Zabihullah Mujahid confirmed that a strike took place on Sunday in Kabul. He strongly condemned the operation, calling it a violation of "international principles."
Zawahiri had been on the run for 20 years since the 9/11 attacks. He took over Al-Qaeda after Osama bin Laden was killed by US special forces in Pakistan in 2011, and had a $25 million US bounty on his head.
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