The deadly riots came after a 12-hour lull of fighting between Israel and Hamas which saw over 200 rockets and mortars fired from the coastal enclave towards southern Israeli communities and over 150 retaliatory strikes by Israeli jets. The Israeli military had no immediate comment on the deaths.
The IDF spokesperson stated that 9000 rioters gathered along the Gaza border fence and threw stones, Molotov cocktails and other explosives.
It was not immediately clear whether the Hamas protests at the border were included in cease-fire negotiations.
Hamas's Al Aqsa TV reported late Thursday that an Egypt-brokered deal had taken hold "on the basis of mutual calm".
It would be the third such truce in a month.
But the deal did not seem to address the deeper issues that have prevented the bitter enemies from reaching a longer cease-fire arrangement.
Rockets fired by Hamas have not killed any Israelis.
At least 160 Palestinians have been killed by Israeli fire since the protests began, one Israeli soldier was killed by a sniper and another officer was moderately wounded after he was shot by a sniper in the Kissufim area in an ambush after troops arrived to disperse a violent demonstration by 20 Palestinian youth close to the border fence. "Following a security assessment", residents can resume their daily routine, the military said.
There was no official confirmation from Israel or Gaza's Islamist rulers Hamas but there were no fresh strikes Friday. A health ministry spokesman says he was shot in the chest in southern Gaza.
A wounded Palestinian girl is brought into al-Shifa hospital on August 9, 2018, following an Israeli airstrike on Gaza City.
It was one of the most serious escalations since the 2014 Gaza war and followed months of rising tensions. Large turnout at the protests has also been driven by widespread desperation in Gaza, amid worsening conditions linked to the blockade.
Two others died in the border clashes, Ali al-Alul, 55, and volunteer medic Abdullah al-Qatati, 21, Gaza's health ministry confirmed.
Another medic, Mohammed Suhwail, tells The Associated Press he witnessed the shooting.
The Israeli fire service says the devices have sparked hundreds of fires and burned some 3,000 hectares. "The second, through the militants who are attempting to approach and attack the border line, is to use the demonstrators as human shields for the group's terrorist ambitions, as well as to provoke a strong Israeli response that will garner headlines and support for their efforts". No Israeli soldiers were injured.