Around 9,000 Palestinians participated Friday in the violent weekly border protest.
The Palestinian health ministry in Gaza said paramedic Abdullah al-Qatiti was killed during the clashes. It said over 300 people were hurt, of whom dozens were shot by Israeli troops.
Israeli men stand next to a auto that was damaged after a rocket fired by terrorists from the Gaza Strip fell in the southern Israeli town of Sderot on August 9, 2018.
The protests came after a deal to end all rocket fire into Israel and air strikes on the Gaza Strip appeared to go into effect around midnight (2100 GMT) on Thursday.
The implication was that Israel had ceased its reprisal attacks in the Strip because Hamas had halted rocket attacks on Israeli communities, but did not see itself obligated to a truce.
The protests along the border dubbed have been the greatest threats to Israeli security in the region since operation Protective Edge due to the combination of terror tunnels, riots, attempted infiltrations and the use of incendiary items.
It said troops responded with tank fire against two Hamas posts, despite the ceasefire between Israel and Hamas, which controls Gaza.
Still, the broader truce held on Friday after a two-day escalation during which the Hamas militant group fired scores of rockets, including a long-range missile deep into Israel, and Israeli aircraft struck more than 150 targets in Gaza.
It was one of the most serious flareups since the 2014 Gaza war and followed months of escalating tensions.
"In light of Hamas statements and the evacuation of Hamas outposts, the Southern Command chose to increase readiness and to close a number of roadways in the Gaza periphery", read the statement released by the IDF Spokesperson's Unit.
The European Union called for an urgent "de-escalation" and warned the two sides are "dangerously close" to a full-blown conflict just four years on from their last war.
Protesters demand the "right of return" to their homes and villages in historical Palestine from which they were driven in 1948 to make way for the new state of Israel.
On Tuesday IDF troops killed two Hamas snipers after the military thought troops came under fire near Beit Lahiya in the northern Gaza Strip.
At least 167 Palestinians have been killed since protests began on March 30.
He said another 25 Palestinians were hit by Israeli fire, with one in critical condition after being shot in the head.