At Neve Dekalim, gunman from several militant factions stormed through after Israeli soldiers left Monday morning, completing the Gaza pullout. Some Palestinians planted a flag from the ruling Fatah movement on the roof of a rabbinical college for Jewish settlers, as others set a fire inside.
The synagogue in the isolated settlement of Morag in southern Gaza was set ablaze minutes after hundreds of Palestinians stormed in.
"They (Israelis) destroyed our homes and our mosques," said a man who gave his name only as Abu Ahmed. "Today it is our turn to destroy theirs."
The synagogues were a focus of Palestinian anger after 38 years of Israeli occupation, primarily because they were among the only buildings left standing. Shortly after removing the last of the settlers two weeks ago, Israel sent in bulldozers to level the houses, leaving only a few public buildings and the synagogues.
In Netzarim, the synagogue was on fire before dawn, with bright orange flames leaping through the roof and the walls.
Helpless Palestinian police stood by and watched, admitting they were outnumbered by the crowds and had little motivation to stop them. An officer who refused to give his name said: "The people have the right to do what they are doing."
Israel TV said crowds of Palestinians entered Kfar Darom in central Gaza and set several fires, including in the synagogue.
As they left their homes last month, the settlers took the sacred Torah scrolls from their synagogues, as well as prayer books and other holy items - symbolizing the end of the use of the buildings as houses of prayer.
Last year Israel's Cabinet ruled the buildings would be torn down. Since the evacuation of the settlers, however, rabbis mounted a high-profile campaign to save the buildings, demanding the government see to it that they would be protected by the Palestinians or by international organizations. On Sunday, the Israeli Cabinet reversed itself, voting not to destroy the synagogue buildings.
The Palestinians refused to protect them, saying they wanted nothing that symbolized the occupation to remain. Early Monday, Palestinian leader Mahmoud Abbas said the structures would be dismantled like all the others.
"They left empty buildings that used to be temples, but they removed all the religious symbols, and they are no longer religious places," he said.
The United States issued a statement criticizing the Israeli change of policy, complaining that it put the Palestinians in a position "where it may be criticized for whatever it does."