Hussam Qawasmeh, a member of Hamas, must also pay $63,000 (£41,000) in compensation to the victims’ families.
Two other suspects were shot dead by Israeli forces in Hebron in September.
The teenagers’ murders in June set off an escalating cycle of violence and led to a 50-day conflict between Israel and Palestinian militants in Gaza.
The leader of Hamas, the Islamist group dominant in Gaza, said in an interview in August that a Hamas cell had killed the teenagers but had not acted on instructions from above.
Naftali Frenkel and Gilad Shaar, both aged 16, and 19-year-old Eyal Yifrach went missing at a road junction between Jerusalem and Hebron as they hitchhiked home on 12 June.
Their bodies were found almost three weeks later in a nearby valley.
The Israeli authorities launched a crackdown on Hamas in the West Bank following the abduction and quickly identified two of the group’s operatives, Marwan Qawasmeh and Amer Abu Aisha, as suspects. They managed to evade capture for several months before being killed.
Hussam Qawasmeh, a 40-year-old Hebron resident arrested in July while attempting to cross into Jordan, was not initially named as a suspect.
However, in August documents were submitted to the Israeli Supreme Court by the Israeli government that alleged he had confessed during interrogation to organising the abduction of the teenagers by obtaining $50,500 (£33,200) in funding from Hamas and purchasing weapons.
He had also admitted to helping bury the teenagers’ bodies on a plot of land he owned and destroying evidence, the documents said.
On Wednesday, he was convicted by an Israeli military court of three counts of accessory to murder, membership of a group that committed murder, two counts of bringing enemy funds into the country, one count of carrying out activities for Hamas, one count of arms dealing, two counts of obstruction of justice and one count of sheltering wanted individuals.
At his sentencing hearing on Tuesday, the Israeli military prosecutor alleged that Hussam Qawasmeh had not seen the teenagers as humans and killed them because they were Jews, the Jerusalem Post reported.
Avraham Frenkel, the father of Naftali Frenkel, said he deserved to be punished in accordance with the full severity of the law.
The court agreed, saying he was guilty of “the cold-blooded and terrible murder of three young people who were going home to their families”.