The troops used sound bombs against Palestinians protesting at Salah e-Din Street, one of the main streets of East Jerusalem.
In December, both the Kerem Shalom and Erez crossings into Israel were closed.
The Palestinian Authority has retained some contact with the Trump administration, despite vowing to cut off all ties to USA leadership in protest of its recognition of Jerusalem as Israel's capital, the London-based Arabic newspaper Al-Hayat reported Saturday.
Speaking to Anadolu Agency, father of detained 16-year-old Palestinian activist Ahed al-Tamimi, Basim al-Tamimi said that at least 500 Palestinians attended protests in the village. The military said forces were conducting searches in a neighboring village for the suspect behind the shooting death this week of an Israeli man when Palestinians hurled a "massive" amount of rocks at them.
More than 100 protesters suffered smoke and gas inhalation.
At least five people in the West Bank suffered injuries when the IDF used rubber bullets to disperse the crowd, Haaretz reports, citing Palestinian health officials.
Violence erupted in Palestinian territories followed the USA decision last month to recognize Jerusalem (al-Quds) as Israel's capital, prompting global condemnation and a United Nations majority vote to reverse it.
According to IDF estimates, some 850 Palestinians participated in clashes in 17 locations in the West Bank and more than 1,000 in four locations along the Gaza Strip's border with Israel.
Palestinians claim east Jerusalem (al-Quds) as the capital of their own state.