No one was injured in the air strikes, which left two large craters, smashed surrounding windows and cut electricity in the heavily crowded camp.
It was the second day in a row in which the army targeted locations near Haniya's home.
On Friday, representatives of Mahmoud Abbas, the Palestinian president, held talks with leaders of Hamas.
"If Hamas and other terrorist groups did not attack Israel there would not have been any destruction"
Yaweh420, West Coast, US
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Abbas wants a halt to rocket attacks on Israel for a month to allow Palestinians to discuss a truce with Israel, and each other.
"This mutual truce would be observed at first for one month in
the Gaza Strip, then afterwards in the West Bank
," said Ayman Taha, a Hamas spokesman, after the meeting.
The armed groups denied that any commitments had been made, saying only that they were weighing the trial Gaza truce proposal.
Taha said his organisation would "study the proposal".
"The next 48 hours will be decisive for determining which way the factions are going, and it will depend on Israel and whether it wants to stop its aggression," said Abdel-Hakim Awad, a spokesman for Abbas's Fatah faction.
Hamas fighters killed
The two Hamas fighters died after Israel's air force destroyed a van in Gaza City, witnesses said.
Earlier air strikes targeted positions used by Hamas and another group, Islamic Jihad.
Israel has carried out dozens of attacks in recent days in retaliation for stepped-up Palestinian rocket fire on southern Israeli towns.
Watch exclusive Al Jazeera footage of Israeli air raid and Nour Odeh's report here
Haniya stayed away from public prayers on Friday, even though Israel denied he was a target of a missile fired at the Shati refugee camp just before midnight on Thursday.
On Thursday, Israel broadened its tactics by rounding up 33 Hamas political leaders in the West Bank.
The most prominent leader arrested was Nasser Shaer, the education minister, who is considered a pragmatist.
Israel has been holding 40 Palestinian politicians from Hamas rounded up over the past year.