Yosef Haim Ben-David, 31, was sentenced for killing 16-year-old Mohammed Abu Khdeir, and was also given 20 years for other crimes. He was also told to pay 150,000 shekels (USD 39,000) to Abu Khdeir's family.
After the verdict was read out, angry members of Abu Khdeir's family cursed Ben-David as he was taken from court.
Ben-David, wearing a burgundy yarmulke and a black shirt, earlier told the court he was "sorry".
"I am sorry for the family. This is not me. I wasn't in control," he said.
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His burned body was found hours later in a forest in the western part of the city.
A forensic report showed smoke in his lungs, indicating he had been alive when set alight.
Ben-David was found in November to have led the assault, but his lawyers submitted last-minute documents saying he suffered from mental illness.
A court rejected the appeal last month, finding him sane.
A court in February sentenced Ben-David's two Israeli accomplices to life and 21 years in prison for the killing, but he was seen to be the ringleader.
"Whatever they decide, our wounds will not heal -- the boy will not come back," he told AFP.
The brutal murder in 2014 shocked Israelis and Palestinians alike, and helped contribute to the escalation in violence that culminated in the 50-day Gaza war that summer in which more than 2,000 Palestinians and 73 Israelis died.
Israeli authorities said the suspects had decided to kill an Arab and equipped themselves with cables, petrol and other materials before randomly choosing Abu Khdeir.
They had tried to kidnap a child in east Jerusalem the day before, but were thwarted by the youth's mother.
"This is an evil and cruel man who does not represent our civilised society," state prosecutor Uri Korb said at the hearing, adding that the killing "brought shame upon our society and offended our values".