The clashes occurred during rallies to mark the 25th anniversary of Hamas, the Israeli news website Ynetnews reported.
In Hebron, a major Palestinian commercial center 19 miles south of Jerusalem, thousands of people marched to the city hall after Friday prayers. In the city's Palestinian section, protesters threw stones at Israeli soldiers patrolling the neighborhood.
Hebron has been tense since a young Palestinian was shot and killed Wednesday. He was threatening soldiers with what turned out to be a toy gun.
Protests were held in 10 other places in the West Bank. No injuries were reported, but at least three military vehicles were damaged.