The Israeli military frequently bombs the Gaza Strip, with civilians being the main target of such attacks.
Palestinians seek East Jerusalem as the capital of their future state in the two-state solution, which would be established in the occupied West Bank and the Gaza Strip.
Israeli troops opened fire on Palestinian protests in Gaza trying to breach the border, killing some 60 people and wounding thousands.
The protests, which have seen unsuccessful attempts to break through the fence, have dwindled since Monday, and the start of the Islamic holy month of Ramadan on Thursday may further dampen interest.
Palestinian security sources said the target was a Hamas base.
Since border rallies began on March 30, more than 100 Palestinian demonstrators have been martyred by cross-border Israeli gunfire, according to the Palestinian Health Ministry.
Israel has accused Hamas, with which it has fought three wars since 2008, of seeking to use the border protests as cover to carry out violence.
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Omar Shakir, the local director for Human Rights Watch, said that if they were unarmed, the identity of the slain protesters and their affiliation to a militant group has little to do with Israel's right under worldwide law to use lethal force at a demonstration. Most of Gaza's residents are descendants of refugees.
There's no sign of a significant easing of the blockade, which was imposed by Israel and Egypt after the 2007 Hamas takeover of Gaza. "This was no peaceful protest", Israeli military spokesman Lt. Col. Jonathan Conricus wrote on Twitter.
Speaking to Al-Jazeera on Wednesday, Hamas's Gaza head Yahya Sinwar warned his movement could return to armed resistance.
On Wednesday, Guatemala followed the US lead, festively opening its new Jerusalem mission with Guatemalan President Jimmy Morales saying his country was bringing a message of "love, peace and fraternity" to Israel.
With Israel lamenting that the Palestinian militants forced it to use deadly force to protect its own people, the IDF dispatched supplies to the aggressors to aid their recovery, but the terrorist-led rioters rejected the generous offer. Paraguay is slated to do the same next week.
Israel occupied the West Bank and east Jerusalem in 1967 and later annexed east Jerusalem in a move never recognised by the worldwide community.
Israeli-Palestinian tensions have been on the rise since December, when US President Donald Trump announced the recognition of Jerusalem as the capital city of Israel, triggering furious protests violently suppressed by the IDF.
Israel regards all of the city, including the eastern sector it annexed after the 1967 conflict, as its capital.