On Sunday, a Palestinian gunman shot dead two Israelis and wounded a third in an industrial park next to an Israeli settlement in the West Bank, and on Thursday the Israeli military said a Palestinian had stabbed an Israeli soldier in the area.
The Israeli military said that the demonstrators, numbering around 14,000, had been "hurling rocks, explosive devices, firebombs and grenades" at Israeli troops and at the fence.
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.
The men subsequently approached an Israeli border post and were shot, the Israeli army said.
Thousands of Palestinians attended the funeral of Aisha al-Rawbi in Biddya village after she was killed when stones were thrown at the auto she was traveling in.
Palestinians in the northern West Bank say a woman has been killed after being struck in the head by a stone thrown by Israeli settlers.
At least 205 Palestinians in Gaza have been killed since protests and clashes erupted along the border on March 30. A Palestinian succumbed to his wounds later, Gaza health officials said.More news: ISS: Space rocket declares emergency after launch - astronauts parachute out
Aisha Mohammed Aravi, 48, was driving in her vehicle along her husband near a West Bank checkpoint south of Nablus late on Friday when they came under attack by Israeli settlers who came onto the road and began throwing large stones at the couple's auto.
The protesters are demanding to be allowed to return to lands now inside Israel, from which their families fled or were displaced during the 1948 war surrounding the creation of the Jewish state.
Qatari-bought fuel began arriving on Tuesday in a bid to alleviate the humanitarian situation in the besieged enclave and prevent any escalation in Israeli-Palestinian violence.
They are also calling for Israel to end its crippling blockade of the strip.
Israel accuses Hamas, which controls Gaza, of orchestrating the protests along the border fence to provide cover for attacks and to distract from Gazas economic plight.
They added that Hamas leader Ismail Haniya also attended the protests east of Gaza City and hailed the ongoing demonstrations.