The clashes took place as the US opened its embassy in Jerusalem, a controversial move that has infuriated Palestinians.
Palestinians see the move as a clear US backing for Israeli rule over the whole city, whose eastern part they lay claim to.
President Donald Trump sent a video message to the opening ceremony, saying Jerusalem move had been a “long time coming”.
The president said: “Israel is a sovereign nation with the right to determine its own capital, but for many years we failed to recognize the obvious.”
He assured the US remained “committed to facilitating a lasting peace agreement”.
Palestinians hurled stones and incendiary devices while the Israeli military used snipers, as black smoke poured from burning tires.
The Hamas-run health ministry said children were among those killed on May 14.
The mass demonstrations, led by Gaza’s Islamist rulers, Hamas, are part of a six-week protest dubbed the “Great March of Return”.
Israel’s army said 35,000 Palestinians were taking part in “violent riots” along the security fence and that its troops were operating “in accordance with standard procedures”.
It said it had killed three people trying to plant explosives near the security fence in Rafah.
Scores of Palestinians have been killed since the protests began. Thousands more have been wounded.
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