Aysenur Ezgi Eygi was taking part in a protest against Jewish settlement expansion in the town of Beita, in the occupied West Bank
Jewish-Israeli activist Jonathan Pollak, who was at the protest, told BBC World Service's Newshour programme he had seen "soldiers on the rooftop aiming".
He said he had heard two separate shots, "with like a second or two distance between them".
"I looked up, there was a clear line of sight between the soldiers and where we were.
In a statement, the Israel Defense Forces (IDF) said: "During Israeli security forces activity adjacent to the area of Beita, the forces responded with fire toward a main instigator of violent activity who hurled rocks at the forces and posed a threat to them.
Damn, she must have been quite strong, to be able to hurl rocks at snipers on a rooftop.