According to the Israeli army, rioters breached the security fence and planted a bomb nearby, setting a section of the barrier alight.
It said all the victims were males aged between 17 and 29.
The terms of the deal saw Doha, a longtime Hamas backer, pledge to pay $60 million (52 million euros) for fuel to be brought into Gaza over six months to supply the strip's sole power plant. It says its troops have used "riot dispersal means" and have fired "in accordance with standard operating procedures".
CNN crews witnessed Palestinians throwing grenades and burning tires, and burning the border fence - with Israeli forces responding with tear gas, live fire and a water cannon.
Israeli army spokesperson Jonathan Conricus said on Twitter an "organised attack" had involved around 20 Palestinians crossing the border after an explosive device destroyed a portion of the fence.
The protests are a continuation of what Gazans dubbed the "March of Return", a series of protests that began in late-March, aimed at highlighting the right claimed by Palestinians to return to homes and villages lost seven decades ago in the war that accompanied the founding of the state of Israel.
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Nearly 1.1m homes and businesses were without power from Florida to Virginia early on Friday, according to utility companies. Hit head-on by Hurricane Michael , homes in this town of about 1,190 people were shattered or ripped from their foundations.
Israel has halted fuel shipments to the Gaza Strip as the regime puts more pressure on the already-besieged coastal enclave. Prior to the delivery, the P.A.'s refusal to allow fuel into Gaza resulted in as few as four hours per day of electricity.
The protests have regularly occurred on Fridays, with as many as tens of thousands of Palestinians gathering at multiple locations along the Gaza fence.
Israeli soldiers have killed more than 200 Palestinians in the clashes, according to the Palestinian Ministry of Health, with thousands of others injured.
Israel accuses the enclave's Islamist rulers Hamas of leading the protests and using them as a cover for attacks.
Hamas chief Ismail Haniyeh, addressing a conference in Istanbul from Gaza, said on Friday that Hamas was seeking to reach understandings with several parties, including Qatar, Egypt and the United Nations.