Officials at Ramallah Hospital say the two, ages 15 and 17, were shot in the upper body by live fire.
Dr Samir Saliba, the head of the hospital's emergency department, confirmed both deaths.
The clashes erupted near a West Bank army checkpoint after dozens of youngsters threw stones at Israeli forces there.
Police spokesman Micky Rosenfeld says border police broke up "disturbances," but did not use live fire.