Hundreds of people were shopping in the market, a spokesman for the Gaza health ministry said.
Hamas, which controls Gaza, had rejected the truce as meaningless.
Meanwhile, Israel said three more of its soldiers had been killed in Gaza.
Palestinian doctors also said that another Israeli air strike after the partial humanitarian ceasefire was announced had killed seven people in Khan Younis.
Earlier, the UN said Israel had attacked a UN-run school housing refugees in Gaza, despite warnings that civilians were there. Fifteen people were killed and dozens hurt.
The White House condemned the attack and said it was “extremely concerned” that Palestinians were not safe at shelters despite being told to evacuate their homes by Israel’s army.
More than 1,300 Palestinians and 58 Israelis have now died in the conflict. Most of the Palestinian deaths have been of civilians.
Fifty-six Israeli soldiers have been killed along with two civilians. A Thai worker in Israel has also died.
The Israeli military said that the three soldiers killed on Wednesday died in a booby-trapped building.
Correspondents say many people in Gaza were unaware the partial ceasefire had been called.
Witnesses at the scene of the market strike in Shejaiya spoke of smoke billowing over the site, with ambulances racing victims to hospital.
A journalist who worked for a local news agency was reported to have been killed.
One witness, Salim Qadoum, told Associated Press: “The area now is like a bloodbath, everyone is wounded or killed. People lost their limbs and were screaming for help. It’s a massacre.”
The Palestinian al-Aqsa satellite TV channel quoted Hamas spokesman Fawzi Barhum as saying that the market attack required “an earth-shattering response”.
The Israeli military had said the ceasefire would last between 15:00 and 19:00.
However, it had warned that the truce would only apply to areas where Israeli soldiers were not currently operating, and it told residents not to return to areas they had previously been asked to evacuate.
Hamas spokesman Sami Abu Zuhri had rejected the truce as meaningless.
“The lull which Israel announced is media exploitation and has no value because it excludes the volatile areas along the border, and we won’t be able to get the wounded out from those areas,” he said in a statement.
Sirens continued to sound in southern Israel after the ceasefire, to warn of militant rocket attacks.
Israel said more than 50 rockets were fired from Gaza on Wednesday.
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