He was hit by a bullet after Israeli forces opened fire in the densely-populated refugee camp following clashes with locals during an arrest raid.
An Israeli soldier was struck by a Molotov cocktail during the clashes and sustained burns.
Al-Jaafari was taken to al-Yamama hospital in nearby al-Khader, where he was pronounced dead.
Medics said the teenager died of internal bleeding, with witnesses at the scene saying Israeli forces stopped ambulances from reaching his body.
The funeral will be held after noon prayers on Tuesday. Mourners will perform prayers in the main mosque in Duheisha camp before walking to the Martyrs Courtyard where al-Jaafari will be laid to rest.
A spokeswoman for the Israeli army said that troops were attacked by people throwing stones and incendiary devices, adding that one soldier was wounded.
“After trying in vain to disperse the crowd of attackers, our forces felt in danger and opened fire at the leader of the rioters, who was hit,” the spokeswoman said, without elaborating.