The military said protesters were "violent, burning tyres and hurling rocks" and that it "will not allow any harm to the security infrastructure or security fence and will continue standing by its mission to defend and ensure the security of the citizens of Israel and Israeli sovereignty, as necessary".
Protester Ahmed Deifallah, 25, said that President Trump's decision to recognize Jerusalem as Israel's capital and move the embassy there "is causing the volcano to spew".
Several thousand people are rallying in Jordan to mark the 70th anniversary of what Palestinians call their "nakba", or catastrophe, when hundreds of thousands were uprooted from their homes in the Mideast war over Israel's creation.
More than two million people are packed into the narrow coastal enclave of Gaza, where poverty and unemployment rates are high. Jordanian, Palestinian, and green Muslim Brotherhood flags flew over the crowd of some 7,000.
The latest bloody attack by Israel came only a few days after President Donald Trump announced that the USA was pulling out of the Iran nuclear accord and would enforce punishing economic sanctions against Iran.
Monday's border march is meant to protest the planned move of the U.S. Embassy in Israel from Tel Aviv to contested Jerusalem that day.
The army forecasts that there will be approximately 10,000 protesters across 17 different sites of confrontation along the border and has stationed 11 battalions to contain the unrest, the senior officer in the southern command told the Haaretz.More news: Kilauea volcano eruption: After lava, Hawaiians brace for acid rain and vog
The latest victim of the Israeli assault on unarmed, peaceful protestors was identified as 40-year-old Jaber Salem Abu Mustafa, who died after being shot in the chest by an Israeli sniper.
Israeli troops fired live bullets and tear gas Friday across a border fence into Gaza, killing a Palestinian man and wounding 146, Gaza's Health Ministry said.
Earlier this week, Hamas's leader in Gaza Yahya Sinwar said he hoped that hundreds of thousands of Palestinians would breach the border fence from Gaza into Israel during next week's protests.
The incursion took place during a weekly mass protest in which thousands of Palestinians gathered along the Israel-Gaza frontier.
Three Israelis who unsuccessfully tried to send an incendiary kite over the border fence, and instead started a fire inside Israel, were detained and held for questioning.
The Hamas-led demonstrations, fueled by despair in Gaza, are part of a campaign to break the blockade imposed by Israel and Egypt after the Hamas takeover of Gaza in 2007. Citing security concerns, Israel maintains tight control over its land and sea borders.