The 31-year-old, viewed as the ringleader, was found to have committed the crime, but the court held off on convicting him after his lawyers submitted a report in recent days arguing his mental state meant he was not responsible for his actions.
Sentencing for the two who were convicted was set for January 13, while a hearing was scheduled for December 20 for the third defendant, Yosef Haim Ben-David, from the Adam settlement in the occupied West Bank.
Mohammed Abu Khdeir, 16, was abducted and killed on July 2, 2014, weeks after the kidnap and murder of three Israeli teenagers in the West Bank.
Signup to our newsletter and follow us on Facebook and Twitter!
The incidents were part of a spiral of violence that led to a 50-day war in the Gaza Strip between Israel and Palestinian militants.
The war killed more than 2,200 people, making 2014 the bloodiest year of the Israeli-Palestinian conflict, according to the United Nations.
Abu Khdeir's father denounced the delay in the verdict for the man accused of being the ringleader and called for the trio's houses to be demolished, as Israel does for Palestinian attackers.
"The court behaves one way with Arabs and another way with Jews," Hussein Abu Khdeir told reporters outside the court, calling the last-minute psychiatric report by Ben-David's lawyers a "trick" and asking why it was not submitted earlier.