The two men, who were not immediately identified, were killed during fresh protests near the Erez checkpoint between Gaza and Israel, the scene of regular confrontation between stone throwing youths and Israeli soldiers in recent months.
Hundreds of Palestinians approached the border crossing shortly before sunset on Tuesday, when the Jewish holiday of Yom Kippur was set to begin.
The protests are part of months of demonstrations against Israel's decade-long blockade of the enclave.
Three Palestinians shot dead in Israel-Gaza border clashes
Since they began on March 30, at least 183 Palestinians have been killed by Israeli fire in Gaza.
One Israeli soldier was shot dead by a Palestinian sniper.
The Erez checkpoint was closed for a week this month after a similar protest damaged the crossing.
Separately, two Palestinians were killed in an Israeli airstrike late Monday night after planting a suspicious device on the border, the Israeli army said.
Israel says its strict measures against Gaza are necessary to isolate the strip's islamic rulers Hamas, with whom it has fought three wars since 2008.
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