Earlier two protesters were killed and 100 wounded during a "day of rage" in the West Bank, Gaza and in East Jerusalem, as Palestinians railed against Trump's controversial move.
One man was killed by Israeli fire in Gaza, while others were injured from tear gas inhalation and rubber bullets, Palestinian officials say.
A second man was shot during clashes.
Muslims are staging protesting around the world after Friday prayers against the US decision to recognise Jerusalem as Israel's capital.
Demonstrations took place in Bangladesh, Malaysia, Indonesia and Kashmir yesterday and hundreds of Palestinians clashed with Israeli security forces in the West Bank cities of Hebron, Bethlehem and Ramallah, the New York Post reported.
Israel has always regarded Jerusalem as its capital, while the Palestinians claim East Jerusalem — occupied by Israel in the 1967 war — as the capital of a future Palestinian state.
Senior Hamas leader Fathi Hammad said earlier that anyone seeking to move their embassy to Jerusalem was "an enemy of the Palestinians".
Speaking before the United Nations on Friday, US ambassador Nikki Haley said the US "recognises the obvious; that Jerusalem is the capital of Israel".
She said the US continued to be "committed to achieving a lasting peace agreement", and accused the UN of bias, saying it "has outrageously been one of the world's foremost centres of hostility towards Israel".