Israel's tactics in confronting the weekly Friday protests have drawn global condemnation.
It comes as US President Donald Trump's special envoy Jason Greenblatt and adviser Jared Kushner visit the region to discuss issues including the Palestinian-Israeli peace process.
Israeli jets bombed 25 targets including Hamas military compounds, the army said.
Minutes later, Palestinians in the Strip launched the first of many rocket and mortar barrages at southern Israel, triggering sirens throughout the area and sending thousands into bomb shelters. Of those, four rockets were intercepted by the Iron Dome anti-missile system while an unspecified number fell in Israeli territory. He said so far the army has fired near those launching the devices and at infrastructure but added Israel has warned it "will not tolerate" the current situation of daily airborne attacks on its territory.
At least 127 Palestinians have been killed by Israeli troops during mass demonstrations and 3,000 have been injured along the Gaza border since March 30. There have been no Israeli fatalities.
"The Hamas terror organisation targeted Israeli civilians throughout the night with a severe rocket attack and is dragging the Gaza Strip and its civilians down a deteriorating path", the Israeli army said.
They were demonstrating in support of what Palestinians say is the right of refugees and their descendants to return to their ancestral homes in what is now Israel.
Hamas, the militant group which rules the Gaza Strip, has not claimed responsibility for the projectile fire.
Israel maintains the use of live ammunition is necessary to defend its borders and stop infiltrations.
Israel accuses Hamas of using the protests as an excuse to carry out attacks on Israel and has responded with both lethal and non-lethal force. It also said around 100 rockets and mortars fired from Gaza either exploded in Israel or were intercepted by air defences. The territory has been controlled by Hamas for more than a decade, during which it has fought three wars with Israel.
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