The boy was arrested Tuesday at a checkpoint near al-Khalil’s Ibrahimi Mosque, Israeli human rights group B'Tselem reported on Thursday.
The five-year-old was then taken into an Israeli military jeep and taken to his parents' house.
The soldiers then took the boy and his father to an army base before eventually transferring them to a Palestinian police station.
At the Israeli base, the father was handcuffed and blindfolded. He said he was interrogated, beaten and fined 5,000 dinars (roughly USD 7,000) for his son’s rock throwing.
"The footage clearly shows that this was not a mistake made by an individual soldier, but rather conduct that was considered reasonable by all the military personnel involved,” B'Tselem Director Jessica Montell wrote in a letter to the military’s legal adviser in the West Bank.
“It is particularly troubling that none of them apparently thought any part of the incident was problematic: Not the fact that they scared a five-year-old boy out of his wits, nor threatening him and his parents to 'hand him over', nor threatening to arrest the father on no legal grounds, nor handcuffing and blindfolding the father in front of his son," she added.
Like in Israel, the arrest or detention of youths under the age of 12 is forbidden in the West Bank, even if they are suspected of perpetrating a crime.