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Mohammed Abu Shamala, Mohammed Barhoum and Raed al-Attar died in the air strike near the southern town of Rafah. They were among six people killed, Palestinian rescue services said.
Hostilities resumed on Tuesday, with each side blaming the other for the collapse of peace talks in Cairo.
Israel has vowed to pursue its campaign until "full security" is achieved.
Six weeks of fierce fighting have left at least 2,103 people dead, all but 67 of them Palestinians and most of them said to be civilians.
The three commanders killed were key to operations including smuggling, tunnel construction and capturing the Israeli soldier Gilad Shalit, the BBC's Yolande Knell reports.
Mr Attar was the most senior commander in the south and was seen taking Mr Shalit from the car and handing him over to the Egyptians during the prisoner exchange in 2011.
Mr Shamala was the Rafah commander said to have been responsible for planning the capture of Mr Shalit.
Mr Barhoum, a close relative of Hamas spokesman Fawzi Barhoum, was a senior local commander.
Israel's military said it had carried out 20 attacks on targets in Gaza during the night in response to militant rocket attacks.
Since the peace talks failed, 213 rockets have been fired at Israel, it added.
There are reports of damage to buildings and possible casualties in other parts of Gaza.
The wife and child of Hamas military commander Mohammed Deif were killed in an Israeli air strike on Tuesday, which he himself reportedly survived.
In another development, Hamas warned foreign airline companies to stop flying to and from Tel Aviv's Ben Gurion Airport from Thursday.