Hundreds of thousands of Palestinians fled or were expelled from what is now Israel, and the border protests are also billed as a "Great March of Return".
The Gaza Strip is controlled by the Islamist group Hamas.
The IDF has described the protests as "a violent riot", saying participants have thrown Molotov cocktails and rocks at soldiers, opened fire on them, set tires on fire to provide cover for attacks and attempted to cross the border into Israel.
The Aljazeera puts the number of protesters wounded at more than 7,000 in total while there have been no Israeli casualties.
However, Hamas now says the militants, including two commanders, were killed "dismantling booby-trapped spying products implanted by Israel through the last decade in Gaza".
At least 350 people have been injured in this weekend's demonstrations, three of them critically, after Israeli forces again fired live ammunition and tear gas at Palestinians.
Last year, PA President Mahmoud Abbas imposed a series of measures against the Gaza Strip that included suspending Palestinian Authority payments to Israel for electricity supplies to the coastal enclave.
The Palestinians were carrying a camera, an axe, a fence cutter, gloves and an oxygen mask, according to the IDF.
The IDF added that during the protests, which began on March 30, "rioters can be seen faking injuries and the exploitation of women and children is rampant".
On the following day, Palestinians mark the "nakba", or catastrophe, to commemorate the anniversary of their mass uprooting during the 1948 war over Israel's creation.
Gaza media reported the explosion was a "work accident", meaning the militants were killed when explosives they were dealing with went off. It failed to elaborate or offer some evidence.
Israel and the West designate Hamas as a terrorist organization.