It is the second USA killing of a prominent militant in the region in months.
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A United States defence official also confirmed to Reuters that the July 26 drone strike killed Saeed.
IS increased its activities in Afghanistan since past year.
This province includes Afghanistan, Pakistan and parts of neighbouring countries was lead by Saeed before he was killed.
Nangarhar has been a hotbed for IS presence since last summer.
“One thing is however, very clear – that Afghan Taliban certainly do not want to deteriorate their ties with Pakistan”, Askari said.
Five U.S. commandos were injured in combat with Islamic State fighters during the offensive, in what officials thought was the first instance of Americans being wounded in fighting against the IS in Afghanistan.
Khan has been reported dead before.
Saeed, a former member of the Pakistani branch of the Taliban who swore allegiance to ISIL, had also been reported killed a year ago, but his death was never confirmed.
On Friday, however, Afghan Ambassador Omar Zakhilwal told Reuters he had seen confirmation from Afghan security forces.
Afghan Taliban have released the crew members of a Pakistani helicopter which crash landed in Afghanistan last week, officials said on Saturday.
The Pentagon Deputy Press Secretary Gordon Trowbridge said the U.S. and Afghan Special Operations Forces conducted operations against the ISIS in southern Nangarhar province between July 1 and 30. Pentagon spokesperson Trowbridge later confirmed the news, but corrected that the target was taken down in the Achin district, instead of Kot.
Kabul also accuses Islamabad of backing Islamic extremists in their country, claiming that the Pakistani military provides sanctuaries to the Taliban and other jihadist groups to launch attacks on Afghan and foreign troops on their soil.
Taliban and al Qaeda are bitter rivals of the Islamic State.
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In Afghanistan, Taliban and Islamic State fighters have battled over territory in Nangarhar, though both have recently been more busy defending against USA and Afghan assaults.
