The raid, involving hundreds of forces, drone strikes and armoured bulldozers, targeted the northern West Bank city of Jenin, a centre for multiple armed Palestinian groups.
Amid the days of violence, a Palestinian attacker in Tel Aviv on Tuesday wounded seven Israelis, two seriously, in a car ramming and stabbing attack before an armed civilian shot him dead.
And overnight, Israel carried out air strikes on targets inside the blockaded Gaza Strip in response to rocket fire from the Palestinian coastal enclave, with no deaths reported.
As the army pulled out of Jenin from late Tuesday, much of the crowded city was left charred and in rubble from the incursion which displaced at least 3,000 residents.
Its adjacent refugee camp, a tiny area home to 18,000 people, has long been a stronghold of militant groups including Islamic Jihad and Hamas.
"The operation is officially over and the soldiers have left the Jenin area," said an army spokesman Wednesday after columns of armoured vehicles were seen withdrawing.
In Jenin on Wednesday, thousands of mourners joined a funeral procession for the slain Palestinians, an AFP correspondent reported.
Militants fired in the air as the bodies were carried through the streets, which were covered in debris from the violence.
"In our souls and blood, we will sacrifice for you, martyr," the crowd chanted.
Jenin residents inspected the widespread destruction in the camp, where gaping holes were torn into buildings, cars were crushed and the ground was littered with bullet casings and broken glass.
Israel's right-wing Prime Minister Benjamin Netanyahu has labelled Jenin and its refugee camp a "terrorist nest", and the army said it had seized arms and explosives depots and militant logistic sites.
The Palestinians labelled the escalation an act of "open war against the people of Jenin".
- 'Camp will remain a terror' -
Islamic Jihad praised its fighters for a "heroic" victory.
"Jenin and its camp will remain a terror that haunts you (Israel)," it said.
Israel has occupied the West Bank since the Six-Day War of 1967 and built many settlements, considered illegal under international law, in the area Palestinians regard as the core on the independent state they are seeking.
Excluding annexed east Jerusalem, the territory is home to about 490,000 Israelis living in settlements -- a number that hard-right nationalist groups within Netanyahu's coalition government are working to increase.
The Palestinians want Israel to withdraw from all land seized in 1967 and to dismantle all Jewish settlements. Netanyahu, however, has pledged to "strengthen settlements" and expressed no interest in reviving peace talks, which have been moribund since 2014.
The army, after a number of deadly attacks early last year inside Israel, started to launch almost daily raids into the West Bank.
The violence has further escalated since Netanyahu's government took over late last year, with clashes concentrated in the northern West Bank, long a hotbed of militancy.
During this week's raid, the army said it had uncovered militant hideouts, arms depots and bomb-making facilities.
"Our troops operated at dozens of sites where terrorists produced ammunition, explosives and various types of weapons," Defence Minister Yoav Gallant said.
"Anyone who attempt to harm the children and the citizens of Israel will experience the full force" of the military, he warned.
The army said troops had "confiscated" a large amount of "terrorist funds" from militants during its operation.
- 'Crimes against our people' -
The Jenin clashes sparked renewed international concern, and the United Nations decried the violence in both Tel Aviv and Jenin.
"The killing, maiming and the destruction of property must stop," UN rights chief Volker Turk said on Tuesday.
Hamas, which controls the Gaza Strip, called the Tel Aviv attack "an initial response to crimes against our people in the Jenin camp".
Medical charity Doctors Without Borders condemned Israeli forces for firing tear gas inside Jenin's Khalil Suleiman hospital.
Palestinian health minister Mai al-Kaila accused the army of shooting at Palestinians in Jenin public hospital's courtyard, saying it marked a moment when "Israel's aggression reached its climax".
The army said reports on the incident are "not currently known to security forces" and added that "terrorist organisations have exploited civilian areas as a hideout".
At least 190 Palestinians, 26 Israelis, one Ukrainian and one Italian have been killed this year, according to an AFP tally compiled from official sources from both sides.
They include, on the Palestinian side, combatants and civilians, and on the Israeli side, mostly civilians and three members of the Arab minority.
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