The $100 million jet sustained significant damage which forced it to jettison its fuel tanks and munitions before returning to base, officials said.
The attack occurred last Tuesday in the Sayid Karam district of eastern Paktia province, much of which is under control of the Taliban. The group had posted a statement on Twitter that evening saying they had downed an enemy jet.
The Taliban has shot down several military helicopters using small-arms fire since their insurgency against US-led NATO forces and government troops began in 2001, but never a fighter capable of super-sonic speeds and reaching a height of 50,000 feet.
The incident underscores the risks foreign forces still face at the hands of the group as Washington extends its military presence in the country beyond 2016.
When contacted for comment, the US military initially said it had no “operational reporting to support the Taliban claims”.
But photographs of the site obtained by AFP and seen by J. Chacko, an open-source military analyst based in London, indicated the jet had lost two “drop-tanks” used to extend flight time, an air-to-ground missile, and two other unguided bombs.
When questioned on the claims, the US military confirmed in a statement to AFP: “On October 13, a US F-16 encountered small arms fire in the Paktia Province in Afghanistan. The surface to air fire impacted one of the aircraft’s stabilisers and caused damage to one of the munitions.
“The pilot jettisoned two fuel tanks and three munitions before safely returning to base. The pilot received no injuries and safely returned to base.”
Chacko, as well as two other military analysts contacted by AFP, said the jet would have had to be flying very low to the ground to be struck by Taliban fire — perhaps as low as a few hundred feet.
Niaz Mohammad Khalil, district governor of Sayid Karam, told AFP that neither US nor Afghan forces had been conducting any operation in the area at the time which have necessitated the use of air cover.