Rescue efforts were hampered by fuel shortages and rolling power cuts that have become more severe in recent months, since Egypt tightened a border blockade of the territory, ruled by the Islamic militant Hamas since 2007.
Israel has also restricted access to Gaza since the Hamas takeover, though it sent diesel fuel for heating and four water pumps during the weekend storm.
Once the storm is over, "the world community needs to bring effective pressure to end the blockade of Gaza," said Chris Gunness, a spokesman for the main U.N aid agency in the territory. Gaza residents "must be freed from these man-made constraints to deal with the impact of a natural calamity such as this," he added.
In the low-lying areas of Gaza, water has been rising since heavy rains began late Wednesday, flooding streets and homes.
One of the hardest hit areas was Nafak Street in Gaza City's Sheik Radwan neighborhood, close to a rainwater reservoir.
Said Halawa, an area resident, said the reservoir overflowed Wednesday evening. By Thursday, water had poured into the ground floor of his two-story home where he and he and 41 other members of his extended family live, Halawa said.
The family called for help and was evacuated by boat from the upper floor. Halawa said he and his family were taken to a makeshift shelter in a neighborhood school. "We got some assistance, some blankets and some food, but I didn't save any of my belongings," said the 52-year-old taxi driver.
At another neighbor school, 30 families found shelter. Children slept on desks and on mattresses on the floor. Some of those at the shelter huddled around wood fires in open-air walkways outside the classrooms to stay warm.
In all, the flooding forced about 40,000 people from their homes, including more than 5,200 who were taken to safety in boats, military trucks or heavy construction vehicles, government officials said.
Another hard-hit area was the refugee camp of Jebaliya in northern Gaza. The local Al Aqsa TV station, run by Hamas, showed Prime Minister Ismail Haniyeh and Interior Minister Fathi Hamad, both of Hamas, touring Jebaliya in a boat.
Housing Minister Yousef Jhariz, who headed the government's crisis team, said the storm caused at least $64 million in damages. One man died from smoke inhalation after burning coal for warmth in his house, health officials said.
By Saturday afternoon, teams were fixing downed power lines and piled up sandbags in some areas to protect homes from flooding.
The storm hit Gaza at a time when it is buckling under the tightened border closure by Egypt. Over the summer, Egypt's military intensified its blockade after ousting Egypt's Islamist president, Mohammed Morsi, a Hamas ally.
Jerusalem and several West Bank towns, meanwhile, were crippled by snow for a third day Saturday. About 28,000 homes in Israel were still without electricity on Saturday, officials said.
Soldiers moved from house to house in some areas of Jerusalem to check on residents. Highways in and out of Jerusalem remained closed to private cars and residents were advised to stay off the roads.