Six others, including at least four fighters, were killed in air strikes and clashes.
Israeli soldiers briefly eased their grip on the northern town of Beit Hanoun, but as darkness fell soldiers began house-to-house searches, local residents said.
The violence followed one of Gaza's bloodiest days in months, when 19 people were killed as Israel continued an operation it says is aimed at stopping rocket fire by Palestinian fighters.
The 12-year-old girl was killed by a single bullet to the head, local hospital workers said.
An Israeli army spokesman said a sniper had spotted an armed fighter and had fired at him but that the girl was killed as the armed man got out of the line of fire.
Another man, said to be a 38-year-old civilian was also shot dead by sniper fire, local residents said.
One fighter was killed in battles with Israeli soldiers backed by tanks near Beit Hanoun, home to some 30,000 Palestinians, witnesses said.
Mahmoud Abbas, the Palestinian president, who has described the operation as a "massacre," called on the UN Security Council to convene to discuss the issue, his spokesman said.
Abbas "sent a message to the head of the Security Council asking him to convene immediately to discuss the tragic situation in Gaza because of Israeli aggression, which has killed 42 Palestinians so far," Nabil Abu Rudeina said.
The violence has put back any resumption of peace talks between Israel and the Palestinians.
Among the dead on Saturday were two Hamas fighters, killed in a missile strike near the Jabalya refugee camp, medical officials said. A 16-year-old boy was also killed in the strike.
Earlier a local Hamas commander was killed in an air raid in Gaza City that wounded four other fighters, medics said.
Some 14 Palestinians were also wounded in various strikes and clashes, hospital officials added.
An 18-year-old civilian wounded by Israeli gunfire earlier on Saturday, later died in hospital, medical workers said.
Three men wounded in the fighting since the offensive, named "Operation Autumn Clouds", began on Wednesday also died of their wounds, hospital workers said.
Israeli forces have killed 45 people in the four-day assault, the Palestinian health ministry said.