Clashes sparked by the abduction and murder of a Palestinian teenager spread from east Jerusalem to Arab towns inside Israel, as autopsy reports showed he was burned alive.
Rocket fire targeting Israel from Gaza also increased, raising fears of an escalation with the Islamist Hamas movement which controls the Palestinian enclave.
Mohammed Abu Khder, 16, was abducted from his Shuafat neighbourhood in occupied east Jerusalem early Wednesday, and his charred body found hours later in a west Jerusalem forest.
Palestinians said Jewish extremists killed him in revenge for the kidnapping and murder in the West Bank last month of three Israeli teenagers.
Clashes following his death and funeral spread Saturday to Arab towns in central and northern Israel, where roads were closed and dozens of demonstrators arrested.
Palestinian news agency Maan quoted attorney general Mohammed Aluweiwi as saying the initial findings of a post-mortem indicated the presence of smoke in the boy's lungs, suggesting he was still alive while being burned.
Abu Khder also suffered a head wound, but that was not the cause of death, Aluweiwi added.
Israeli police said they still could not confirm the motive for Abu Khder's murder.
A spokeswoman told AFP police were investigating "all possibilities", and that there was a gag order on all details of the investigation.
The teenager's funeral on Friday, attended by thousands of mourners, led to a third straight day of clashes across Israeli-annexed Arab east Jerusalem.
Police reported disturbances in the Arab towns of Taibe in northeast Israel and Jaljulia and Qalansuwa in the centre on Saturday, also spreading to Umm el-Fahm, Arara and Nazareth.
But despite the violence, Israel did not consider it the beginning of a popular Arab-Palestinian uprising.
"I don't see a third intifada here," Internal Security Minister Yitzhak Aharonovitch told Channel 2 television during a tour of the north.
The road between Taibe and Tira stayed closed on Saturday, while a route near Qalansuwa was shut for several hours.
Police said one officer was injured by a stone near Arara, and around 35 Arab Israeli suspects had been arrested in clashes since Friday night.
A further 25 Palestinians were arrested in east Jerusalem and nearby West Bank clashes.
One of those arrested in east Jerusalem was Tariq Abu Khder, a 15-year-old cousin of the murdered Palestinian youth and an American citizen currently on holiday.
Speaking to AFP, his parents said Tariq was arrested in Shuafat after being beaten by police on Thursday.
A video circulating on social media (https://www.youtube.com/watch?v=HDENWwEDGr4) shows what appears to be Israeli border police beating and kicking a handcuffed semi-conscious figure before dragging him away.
The parents, who saw their son in an Israeli hospital, said they were told Tariq had been arrested for being masked.
Police spokeswoman Luba Samri could not confirm it was Tariq in the video, but said the footage was from the arrest of a group of six Palestinians, including Tariq.
The justice ministry, meanwhile, said it was investigating the video.
Samri said police found a sling on Tariq, who had attacked police and resisted arrest, while others were throwing stones and Molotov cocktails, wounding six police.
Abu Khder will appear before a Jerusalem court on Sunday, his parents said.
US State Department spokeswoman Jen Psaki said the United States was "profoundly troubled" by the reports that he was "severely beaten" while in police custody and "strongly condemn(s) any excessive use of force".
"We are calling for a speedy, transparent and credible investigation and full accountability for any excessive use of force," she said.
Militants fired more rockets and mortar rounds at Israel from Gaza amid continued Egyptian efforts to broker a truce following a flare-up of cross-border violence.
The army said at least 18 rockets and mortar rounds were fired at southern Israel on Saturday, lightly wounding one soldier.
Four rockets were intercepted by the Iron Dome anti-missile defence system over the cities of Beersheba and Ashkelon, the army said.
The military "targeted a terrorist attempting to launch rockets," it said late Saturday, while Gaza medics said two Palestinians were wounded east of Rafah.
Earlier, Israeli warplanes attacked three sites in southern Gaza, targeting training camps of Ezzedine al-Qassam Brigades, Hamas's military wing, in Rafah and Khan Yunis, as well as an empty field in Khan Yunis.
Palestinian sources said there were no injuries.
There has been a surge in militant rocket fire and retaliatory Israeli air raids since the kidnapping and murder of the three Israeli teenagers prompted a huge crackdown on Hamas in the occupied West Bank.