The troops were jubilant as they withdrew, reports say
The pursuit of Mr Zeevi's killers is the key reason given by Israeli officials for the continuing occupation of six Palestinian towns in the face of a US demand to pull back.
United Nations Secretary-General Kofi Annan added his voice to the US demands on Wednesday, expressing concern at what he called a "dangerous escalation" in violence.
The Palestinians, who talked of a "bloody massacre", said that more than nine people were killed in the dramatic raid on Beit Rima and dozens wounded.
Israeli radio said that two of 11 suspected Palestinian militants arrested in the village belonged to the cell that killed Mr Zeevi on 17 October, while a third member was still at large.
The radio named the detainees as Salah Halawi of Azzaryeh village in the West Bank and Mohammed Rimawi of Beit Rima.
It said the actual killer, Hamdi Ghuran, had recruited both men two months before the killing.
Bloodbath
The village near Ramallah was sealed off after the operation, during which tanks and infantry combed the village as a loudspeaker warned villagers in Arabic not to resist.
Israel says the Palestinians who died were gunmen killed in fighting. But Palestinian sources say they were policemen guarding the village who were shot without warning.
The Israelis kept media and Palestinian emergency services away from Beit Rima all day, adding to the confusion.
But a doctor in Beit Rima told the BBC by telephone that he had seen six bodies lying in the streets in the village and had heard that many more were lying in olive groves nearby.
Villagers said the troops made house-to-house searches and used bulldozers to demolish several houses.
As the operation in Beit Rima was under way, Prime Minister Ariel Sharon told parliament that Israeli forces would leave Palestinian towns as soon as they had finished their security operation.
The Palestinian leadership reacted by calling for American and international pressure on Israel to "immediately put an end to this continuous aggression and offer protection for Palestinian civilians".
US Secretary of State Colin Powell repeated the US call for Israel's "immediate" withdrawal from Palestinian areas.
"It's a very volatile period and I would like to see this start moving in the other direction," he said.
Day of violence
Israeli soldiers also shot dead three Palestinians in Tulkarm on Wednesday, saying the men were about to open fire. Palestinian sources said it was an Israeli ambush.
A Palestinian was also shot and killed by Israeli soldiers in Abu Dis on the outskirts of Jerusalem.
The 25-year-old was throwing firebombs at soldiers when he was shot in the face and eye with
rubber-coated steel bullets, Israel army radio reported.
In another incident, six Palestinians were injured near Hebron when a vehicle they were travelling in was sprayed with machine-gun fire on a by-pass road used by Jewish settlers.
Dozens of Palestinians have died since Thursday when Israel reoccupied parts of six towns in response to the assassination of Zeevi, known as an Israeli hardliner.
The United States fears the upsurge in Middle East violence could interfere with its coalition to defeat international terrorism by alienating moderate Arab states.
In all, more than 900 people have died in violence related to the 13-month Palestinian uprising against Israel's occupation, including more than 700 Palestinians and 175 Israelis.