The demonstrations in Gaza and the West Bank were prompted by President Donald Trump's recognition of Jerusalem as Israel's capital on Dec. 5.
The Israel Defense Force said about 2,000 Palestinians were involved in nine separate protests on the border between Gaza and Israel. Some threw stones and incendiary weapons and Israeli troops responded with tear gas and bullets, seriously injuring four people, a Gaza health ministry spokesman said.
In the West Bank, about 500 demonstrators burned tires and threw stones and burning bottles at troops in at least 30 locations.
At least 56 people were injured in the clashes.
Tensions in Gaza and the West Bank have increased since Trump's controversial announcement, and they were ratcheted up Friday when three missiles were fired into Israel from Gaza.
The missiles marked the first attacks on Israel from Gaza since a two-week rocket barrage on Dec. 18.
Although the sources of the Friday missile launch remains unknown, officials said they were intercepted by the Israeli Iron Dome defense system, and prompted an immediate reaction from the Israeli military.
Israeli tanks and aircraft targeted two Gaza military posts of Hamas, the paramilitary wing of the de facto government of Gaza. Six Israeli missiles were fired, the Palestinian news agency Wafa reported.
A witness told Al Jazeera that plumes of smoke were visible near the Gaza City neighborhood of al-Tuffah.
A spokesman for Gaza's Hamas-run health ministry said the Israeli attack did not cause any injuries.