The ministry named the dead men as Karim Abu Fatayer, 30, shot near the central Gaza Strip town of Bureij and Sadi Moamer, 26, killed near Rafah, in the south. It said that both men were shot in the head.
At least 270 other Palestinians were wounded, 70 of them by gunfire, the ministry said.
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The Israeli military did not know of any deaths but said that troops had opened fire in border incidents.
At least 171 Gazans have been killed by Israeli fire since late March, mostly during border clashes and protests.
One Israeli soldier was shot dead by a Palestinian sniper in July.
Israel and Palestinian militants in Gaza, including its Hamas rulers, have fought three wars since 2008 and tensions since late March have led to fears of yet another full-blown conflict.
There have been three intense flare-ups since July, the latest on Thursday, when Israel responded to some 180 rockets and mortars fired from Gaza with widespread air strikes.
An Israeli official said on condition of anonymity Wednesday that truce talks mediated by Egyptian and United Nations officials had reached an initial set of 'understandings' leading to calm on the border over the past few days.
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Senior Hamas official Khalil al-Hayya told AFP on Friday that a durable truce with Israel was near. "In my opinion, yes, we are nearing an agreement," he said.
He added that the UN and Egyptian talks taking place in Egypt with various Palestinian factions have "taken a big step forward towards understandings with the occupation... and the possibility of restoring calm".
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