"Justice has been delivered. This terrorist leader is no more," Mr Biden said from the White House.
Osama bin Laden's former deputy had been on the run for 20 years since the September 11, 2001, attacks on the US that he is believed to have helped mastermind.
The Egyptian surgeon, 71, grew up in a comfortable Cairo household before turning to violent radicalism.
Al Zawahiri took the helm of Al Qaeda after bin Laden was killed in a covert US military raid in Pakistan in 2011.
A senior administration official said the US strike was conducted by a drone that fired two Hellfire missiles into the third floor of Al Zawahiri's Kabul home — killing him, but no one else.
"We are confident through our intelligence sources and methods including multiple streams of intelligence that we killed Zawahiri and no other individual," the official said.
The strike was conducted by the "US government", the official said. US outlets said the CIA had carried out the strike early on Sunday.
This is the first known US strike in Afghanistan since a failed drone attack in Kabul killed 10 civilians on August 29 last year, as the US rushed to leave the country after 20 years.
The US had said it would retain "over-the-horizon" strike capability despite no longer having a troop presence in Afghanistan.
With other senior Al Qaeda members, Al Zawahiri plotted the October 12, 2000, attack on the USS Cole navy ship in Yemen, which killed 17 US sailors and injured more than 30, Mr Biden said.
He was indicted in the US for his role in the August 7, 1998, bombings of the US embassies in Kenya and Tanzania that killed 224 people and wounded more than 5,000.
"He carved a trail of murder and violence against American citizens, American service members, American diplomats and American interests," Mr Biden said.
"Now, justice has been delivered and this terrorist leader is no more. People around the world no longer need to fear the vicious and determined killer."
The news comes just weeks before the first anniversary of the final withdrawal of US troops from Afghanistan, leaving the country in the control of the Taliban insurgency that fought western forces over the preceding two decades.
The US withdrew after the Taliban signed the deal in Doha in 2020 in which they promised not to allow Afghanistan to be used again as a launchpad for international terrorism.
But experts believe the group never broke their ties with Al Qaeda and the fact that the strike took place in central Kabul suggests the Taliban knew where Al Zawahiri had been staying.
Taliban spokesman Zabihullah Mujahid said on Twitter that an attack was "carried out by American drones" and condemned the action.
“Such actions are a repetition of the failed experiences of the past 20 years and are against the interests of the United States of America, Afghanistan and the region,” Mr Mujahid said.
Al Qaeda has built up its presence in Afghanistan after US forces left the country in August last year, US Central Command chief Gen Frank McKenzie said last December.
Other US defence officials had also warned of a resurgence of Al Qaeda and other extremist groups in Afghanistan under Taliban rule.
Aaron Zelin, a fellow at the Washington Institute for Near East Policy, said Al Zawahiri had a mixed reputation as Al Qaeda leader, with many regarding him as incompetent, mainly because of the proliferation of ISIS on his watch.
Mr Zelin said there was no obvious successor given that Al Qaeda has become increasingly decentralised, with many of its leaders no longer in Afghanistan and Pakistan.
“It'll really test the coherence of the organisation,” he told The National.
“The fact that the senior leadership is not all based in the same area, but spread out between South Asia, the Middle East and Africa.
"It could take a minute for them to at least publicly declare who the next leader is.”
Al Zawahiri had been on the FBI's most wanted terrorist list for conspiracy to murder US nationals, and the US State Department offered a $25 million reward for information on his whereabouts.
For years, his death has been rumoured but he recently appeared in an April video praising an Indian Muslim student who wore a hijab in a protest against a ban against the traditional Islamic head covering.
Mr Biden is still in isolation after a Covid-19 infection and spoke from a balcony at the White House.
- With additional reporting by AFP