Later on Friday, medics said that Israeli troops fired tear gas and live bullets at Palestinians taking part in the protests, injuring at least 100 people.
The Israel Defense Forces (IDF) on Saturday inflicted a warning air strike on a group of Palestinians in the Gaza Strip, which were preparing to send a batch of explosive balloons over the border into Israel, a IDF spokesperson said.
The protests tapered off around sunset when many demonstrators left border camps for the evening meal that breaks their fast during the Muslim holy month of Ramadan.
Ashraf al-Qedra, the health ministry spokesman in Gaza, told reporters that Zeyad al-Briem, 25, and Haytham al-Jammal, 15, were killed in east of Khan Younis in southern Gaza Strip, while Emad Darabieh, 26, was shot dead in east of Jabalia in northern Gaza.
French news agency Agence France Press said one of its photographers, Mohammed Abed al-Baba, was wounded at a mass rally after Israeli forces opened fire.
In Gaza, at least 115 Palestinians had been killed and almost 3,800 wounded by Israeli army fire in previous protests near the border fence.
Israel's use of potentially lethal force against the protesters has drawn worldwide criticism.
On Friday, the Israeli army said in a statement that it had repelled about 10,000 Palestinians who converged on five sections of the border.
Israel sees the BDS movement as a strategic threat and accuses it of anti-Semitism - a claim activists firmly deny, calling it an attempt to discredit them.
The UN General Assembly will hold an emergency meeting next Wednesday at 3 p.m.to vote on an Arab-backed resolution on Gaza, the body's President Miroslav Lajcak announced Friday.
"Unfortunately, some Arab leaders in the region have betrayed the great nation of Palestine by staying silent against the US aggressive and adventurous move [in relocating its embassy to Quds] and establishing ties with the Zionist regime", the army's statement said, adding, "but they must know that the nations of the world are watching them and history will remember [their betrayal]".
On Thursday Israel dropped leaflets in Gaza urging Palestinians not to take part in protests or try to breach the fence on Friday, "and not to allow Hamas to use you for its narrow factional interests, which Iran is inspiring". He said the demonstrations would continue until Palestinians achieve their demand for a right of return to ancestral lands. They pledged to continue raising voice for rights of oppressed Palestinians and rejecting nefarious designs of Israel and United States against people in various parts of the world including Palestine. Israel and Hamas have fought three cross-border wars since 2008.
Two million Palestinians have sunk into poverty as Israel and Egypt, citing security needs, clamped down on Gaza's borders.
Israel has long refused to admit Palestinian refugees from the 1948 war or their millions of descendants, saying that would spell demographic suicide and that they should stay in a future Palestinian state.
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