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.
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.
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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.
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 begin 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.
Another 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 shows what appears to be Israeli border police beating and kicking a handcuffed semi-conscious figure before dragging him away.