But Israeli and US officials were determined not to let the violence diminish the embassy celebration.
The numbers are expected to rise.
Later in the day, Israeli leaders and a United States delegation including treasury secretary Steven Mnuchin and President Donald Trump's daughter and son-in-law, Ivanka Trump and Jared Kushner, were due to attend the opening of the embassy.
Ismail Radwan, a senior Hamas figure, said the mass border protests against Israel will continue "until the rights of the Palestinian people are achieved". "Because when President Trump makes a promise, he keeps it".
The clashes took place as a White House delegation and Israeli officials gathered for the embassy inauguration ceremony in Jerusalem.
Likewise, Mr. Trump's aides also made no direct reference to the climbing death toll. "Today we open the United States embassy in Jerusalem Israel", he said to warm applause. They view the relocation of the United States embassy as a one-sided move that invalidates America's role as an impartial peace broker in the region.
Israeli Prime Minister Benjamin Netanyahu, however, praised the USA president for having made "history". "In such a reality in particular, it is good that the leader of the free world is President Trump".
"There is no greater supporter of Israel on the earth", he said.
"Congratulations!" tweeted President Trump. "This city and its entire nation is a testament to the unbreakable strength of the Jewish people".
Israelis have already honored Trump with a public square near the embassy to be named in his honor.
The U.S. delegation was welcomed by Netanyahu and his wife Sunday night with a gala.
Black smoke from tyres burned by demonstrators rose into the air at the border.
"This disproportionate and illegal use of lethal force against unarmed civilian protesters is criminal", the Palestinian Foreign Ministry said in a statement.
By midafternoon, at least 52 Palestinians, including a 14-year-old boy, were killed while at least 772 were wounded, including 27 critically, Palestinian health officials said.
Israel's military dropped leaflets into the enclave on Monday, warning Palestinians "not to serve as a tool of Hamas" or approach or damage Israel's frontier fence.
"If you're not prepared to recognize that Jerusalem is the capital of Israel, and that's where the American Embassy should be, then you're operating on a completely different wavelength".
The eyes of the world are on the Middle East on Monday with the new U.S. Embassy opening in Jerusalem. "These deplorable and unacceptable measures deliberately undermine all peace efforts", Palestinian president Mahmud Abbas says.
Nabeel Shaath, a long-time Palestinian peace negotiator, thinks Trump set the peace process back.
"Israel is a sovereign nation with the right like every other sovereign nation to determine its own capital", President Trump said in a taped message played at the dedication ceremony.