"The Israelis and their American friends are dancing. They are celebrating while my people have dug 58 more graves just today," Dr Ramzy Baroud said.
"They have danced on our graves for far too long."
More than 2700 Palestinian protesters were injured but Israel has defended its actions, saying troops were defending its border.
It also accused Hamas militants of trying to carry out bombing and shooting attacks under the cover of the month-long mass demonstrations.
More than 100 Palestinians have died since they began on March 30, which Dr Baroud labelled as "absolutely horrific".
"I was born and raised in Gaza, so many of these people are people that I know," he said.
"No words can describe the feeling."
The rally marks the 70th anniversary of what Palestinians call their "nakba" or catastrophe - the uprooting of hundreds of thousands in the Middle East war over Israel's 1948 creation.
Fouad Charida was an eight-year-old boy when he was separated from his family in the chaos of dispossession in May that year, only to be found "like a stray cat looking for food in the rubbish" a few weeks later in south Lebanon.
"I am standing here in front of you as a survivor of a brutal massacre committed in my village 70 years ago," he told the Town Hall rally.
The Palestinians, who seek east Jerusalem as their capital, have cut off ties with US President Donald Trump and insist his administration is unfit to serve as a mediator in future negotiations on the city's final borders.