"Nakba Day" is when Palestinians annually commemorate what they describe as the "catastrophe" they experienced when Israel was established in 1948.
Thousands of Palestinian protesters joined the demonstration in eastern blockaded Gaza Strip.
A year ago Israeli snipers killed 60 people in a day at the Gaza frontier as thousands came out to protest against the opening of the USA embassy in disputed Jerusalem, part of which Palestinians claim.
Groups approached the border fence, planting Palestinian flags and throwing stones toward Israeli soldiers on the other side despite the efforts of marshalls in orange vests to keep protesters away from the barrier, witnesses said.
"The rioters are setting tires on fire and hurling rocks", the Israeli military said as the unrest transpired. They will provoke and attack Israeli border forces in hopes of drawing fire, which they will then position in worldwide media as an unprovoked attack on peaceful demonstrators.
"Today also marks the seventy-first anniversary of the Palestinian Nakba", he said "On this solemn day, the Palestinian leadership reaffirms its commitment to achieving justice and securing redress for decades of injustice and brutality exercised against the Palestinian people".
They also carried keys signifying their determination to return to their original homelands, now occupied by Israel, which they were forced out from in 1948.
This year's protests came two weeks after a deadly flare-up between Gaza militants and Israel which threatened to spill into a new war.
The attacks on Wednesday came on the same day the United Nations reported that the effects of the USA cutting aid to Palestine will result in 1 million people facing severe hunger in the next month.
This year, Palestinian leaders in Gaza called for a general strike and border protests on Wednesday.
The European song contest kicked off in the Israeli capital Tel Aviv on Tuesday amid the reported deployment of the country's Iron Dome anti-rocket systems. The reports said further the army closed down all roads that lead to the area of the fence of the border with the Hamas-ruled coastal enclave.