"The Shin Bet, with the assistance of the army and the police, have arrested a number of those involved in the murder of Sarya Ofer," the Shin Bet agency said in a statement.
It was not yet known if Friday's killing was politically motivated.
The Shin Bet said Odeh Farid Harub, 18, and Bashir Ahmed Harub, 21, had confessed to the killing of the retired army colonel at his isolated Jordan Valley home.
They were among three men from the southern West Bank village of Dir Samat, near Hebron, arrested on Saturday "following intelligence information."
The suspects allegedly told interrogators they had gone to the compound that Ofer shared with his wife Monique late one night about two weeks ago but without doing anything.
The Shin Bet said their account matched a statement by Monique, who escaped with injuries after her husband was bludgeoned to death, and who said youths from the Hebron area had come to the house "under suspicious circumstances."
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Police said after the killing that it was most likely the work of Palestinian militants, while rightwing Israeli politicians said peace talks with the Palestinians should be suspended as a result.
But media have speculated that the killing could have been the result of a bungled burglary attempt or the settling of a personal dispute.
"The investigation is under way and the motive for the murder is still being checked," the Shin Bet said.
Several Israelis and Palestinians have been killed or wounded in a recent spate of violent incidents in the occupied territories.
Suspected Palestinian attackers wounded a nine-year-old Israeli girl in a settlement near Ramallah on October 6, and two Israeli soldiers were killed in separate incidents in the West Bank on September 21 and 22.
Israel's army shot and wounded a Palestinian who was trying to cross a security fence from the West Bank into Israel on October 8, a week after soldiers shot dead a Palestinian in the Gaza Strip near a border fence in the north of the blockaded territory.