The disturbances broke out when an Israeli army unit on Sunday carried out its latest raid in the West Bank town, where a curfew was imposed, Palestinian security sources said.
They said about 15 jeeps or armoured vehicles took part in the operation, which triggered stone-throwing protests by Palestinian youths.
Gunshots were also heard, but there were no reports of casualties.
“Israeli vehicles raided the town of Jenin on Sunday at 6.00 a.m. (GMT 3.00 a.m.), imposing a complete closure on the city and its refugee camp, claiming that Palestinian resistance fighters are based there,” Aljazeera's correspondent reported.
“Israeli forces have brought all the town's facilities to a complete close, shutting all schools and universities,” he said.
Palestinian security sources said soldiers were searching houses in Jenin for wanted resistance fighters or arms, the sources said.
An Israeli army spokesman said the raid was part of a "series of operations conducted on a regular basis over the past two weeks in Jenin against terrorist infrastructures."
Aljazeera's correspondent said the operation may thwart plans in the town to commemorate the third anniversary of the Al-Aqsa Intifada.
"Israeli forces have brought all the city’s facilities to a complete close"
Israeli forces carried out a similar raid on Jenin on 21 September.
Israel also claimed that it had arrested eight Palestinians were overnight on suspicion of involvement in anti-Israeli attacks.
Five of the arrests took place in Dura, near the southern West Bank town of Hebron near where a fighter infiltrated a Jewish settlement on Friday, killing an Israeli man.
The fighter belonged to the resistance group Islamic Jihad and came from Dura, Palestinian security sources said.
A baby girl also died in the firefight.
Mahmud Hamdan, 22, was later shot dead by troops and his body taken to a Hebron hospital to be claimed by his family.
The sources said Hamdan was released two months ago from an Israeli prison after serving a 14-month term.
In the Gaza Strip, five mortars were fired early on Sunday at the industrial zone of the Jewish settlement bloc of Gush Katif, but without causing casualties or damage, the army spokesman said.