Israeli Air Force planes targeted a Hamas military base in the southern Gaza Strip on Tuesday night after a rocket was sacked from the Gaza Strip into Israel.
However, the Israeli army on Tuesday denied it carried out the air strike, according to reports.
Tuesday's deaths came amid tensions between Palestinians and Israeli forces following US President Donald Trump's announcement he would move the American embassy in Israel to Jerusalem and recognise the city as Israel's capital.
Residents who witnessed the incident identified the two men as members of the Islamic Jihad militant group.
Israeli planes and tanks shelled the Palestinian territory on Monday after the rocket strike, in what was the latest in a series of cross-border exchanges that have left at least four Palestinians dead.
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The control Hamas exercises over the Gaza Strip was evidenced as Israel once again destroyed a terror tunnel that extended from the Hamas-ruled territory into Israel, The Jerusalem Post reported Sunday.
Later Tuesday night, a "projectile" was sacked from Gaza towards southern Israel, the army said in a statement, without further details.
The last week has seen the largest number of rockets fired at Israel from the Strip since the 2014 Gaza war.
The air force fired missiles into a site, run by the al-Qassam Brigades, the armed wing of Hamas, southwest of Khan Younis, in the southern part of the Gaza Strip. No casualties were reported on the Israeli side.