Police had previously identified the suspects as Assad Yussef Assad Al-Rafa’i, 19, and Subhi Imad Subhi Abu Shakir, 20.
According to a police statement on Friday, both are residents of Romana village in Jenin province.
The arrests came after a manhunt involving helicopters, roadblocks and vehicle checks.
The three men killed in the attack died at the scene and were buried on Friday after a huge funeral procession, Israel Rescue Service Zaka Tel Aviv said.
The Magen David Adom (MDA) emergency services named her Oren Ben Yiftach, a father of six; Yonatan Habakuk, a father of five; and Boaz Gol, a father of five. All were in their 40s, the MDA previously said.
Three men injured in the attack are now in a stable condition, the treating hospitals said on Sunday.
The two patients at Beilinson Hospital are on ventilators and anesthetized, the medical center said, describing their condition as “serious but stable.” The condition of the injured 20-year-old at Sheba Medical Center has not changed, the hospital said, saying he is “stable but critical with serious head injuries from an ax.”
Elad, where the attack took place, is a quiet, small and largely religious town in central Israel, not far from Ben Gurion International Airport.
The attack was the latest in a series of violent incidents that have gripped Israel and the Palestinian Territories in recent weeks.
Dozens have died in violence in Israel and the West Bank since March 22, according to a CNN tally.
In a statement, Prime Minister Naftali Bennett condemned Thursday’s attack and offered his condolences to the families affected.
“Our enemies have launched a murderous campaign against Jews wherever they are. Their goal is to break our spirit, but they will fail. We will get our hands on the terrorists and their support environment and make them pay the price,” Bennett said in the statement.
Israel confirmed that it will keep Gaza and the West Bank under lockdown at least until Monday after the attack and will extend existing closures for Israeli public holidays.
The Israel Defense Forces said Palestinians living in those areas would only be allowed to enter Israel with prior authorization on humanitarian grounds, under special circumstances or for medical reasons.
Palestinian Authority President Mahmoud Abbas also condemned the violence on Thursday, his office said in a statement.
“The killing of Palestinian and Israeli civilians only serves to further worsen the situation at a time when we are all striving to achieve stability and prevent escalation,” Abbas said in the statement.
Abbas warned that Jewish settlers were using the incident as a pretext “to carry out attacks and responses against our Palestinian people.”
He added that “lasting, comprehensive and just peace is the shortest and best way to ensure security and stability for the Palestinian and Israeli peoples and the peoples of the region.”
Late Thursday, Palestinian militant groups in Gaza, Hamas and Islamic Jihad praised the alleged terrorist attack without explicitly acknowledging it.
Hamas spokesman Fawzi Barhoum linked the attack to clashes at the Al-Aqsa Mosque compound in Jerusalem.
Only Muslims are allowed to visit the holy site, called the Temple Mount by Jews and Haram al-Sharif or Noble Sanctuary by Muslims, during the last 10 days of Ramadan each year. Groups of Israeli Jews began visiting again on Thursday.
CNN’s Jennifer Hansler and Jorge Engels contributed coverage.