The verdict of another trial was also announced, acquitting their 40-year-old friend on identical first-degree murder and arson charges.
The conviction of Alex King, 13, and Derek King, 14, carries a maximum sentence of life in prison with the possibility of parole. They were originally charged with first-degree murder, which carries an automatic sentence of life without parole.
The jury opted for the lesser charge after five hours of deliberation. Sentencing was set for Oct. 17.
The boys showed no emotion as the verdict was read.
Alex King, 13, and Derek King, 14, who were 12 and 13 at the time of the slaying Nov. 26, were charged with killing their father, Terry King, 40.
Ricky Chavis, 40, faced the same charges as the boys. He was the defendant in a separate trial that was held Aug. 26-30. That verdict was sealed until the boys' trial was completed. He shook his attorney's hand and wiped his moist eyes after the innocent verdict was read.
Chavis, a convicted child molester who allegedly had sexual relations with Alex King before the murder, also faces charges of accessory after the fact and evidence tampering. He faces trial on those charges later this year.
Derek and Alex King said Chavis committed the murder and told them to confess, convincing them that as juveniles nothing would happen to them. A grand jury, however, charged them as adults.
Chavis has said the boys committed the murder because Alex was afraid his father would stop him from seeing the older man. He did not testify.
David Rimmer was the prosecuting attorney in both trials, essentially placing him on both sides of the issue. At least two prominent attorneys -- Roy Black of Miami and former U.S. Attorney Kendall Coffey -- have called the case an ethical problem and one of the low points in the history of the Florida justice system.
But the basic problem was cleared by Chavis' acquittal.
Rimmer defended his actions after the trial.
"The boys testified under oath to the grand jury that Chavis, and it was up to the trial jury to decide if they believed them. They apparently did not," Rimmer said.
Rimmer said Chavis was tried last week because the defendant had asked for a speedy trial and the deadline was the day the trial started.
There is also criticism of the national television of the trial on Court TV because of the boys' age and cherubic appearance.
In closing arguments Thursday, the defense cited a lack of evidence and urged acquittal, and the prosecution the boys had a motive.
The boys had originally confessed to the killing, but recanted during the Chavis trial and again during their own trial.
Rimmer argued that there is no way the boys could have been coached for their confessions to include the kind of details they provided.
Defense attorney James Stokes, representing Alex, said there was absolutely no physical evidence linking the boys to the beating.