The International Security Assistance Force (ISAF) identified Ismail Jan as deputy to the senior Haqqani commander inside Afghanistan and said he was killed in the eastern province of Paktya on Wednesday.
It was not possible to confirm Jan's death or position independently and ISAF provided no immediate details on how they knew he had been killed.
Security forces tracked his location based on intelligence reports from Afghan government officials, citizens and "disenfranchised insurgents" before calling in the air strike, ISAF said in a statement.
The US-led force accused Jan of providing material support for Tuesday's attack on the Intercontinental in the Afghan capital, frequented by Westerners and Afghan government officials.
The strike comes two days after a senior US military officer said that Pakistani leaders show no sign they are ready to crack down on Haqqani militants operating from sanctuaries near the Afghan border, despite repeated US requests.
Heavily armed militants stormed the hilltop hotel late Tuesday, sparking a ferocious battle involving Afghan commandos and a NATO helicopter gunship that left at least 21 dead including the nine attackers.
The Taliban claimed responsibility for the attack, but NATO said it was carried out in conjunction with the Haqqani network, blamed for previous attacks in Kabul and considered the most potent US enemy in the east.
NATO said Jan and "several" other Haqqani fighters were killed the following day in Paktya, which borders Pakistan's tribal belt where the Haqqani leadership is based in the semi-autonomous district of North Waziristan.
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