RUF leaders Issa Sesay, 38, and Morris Kallon, 45, were convicted of 16 of the 18 charges, while Augustine Gbao, 60, was found guilty on 14 of the counts.
The Freetown trial of the RUF rebel leaders, related to Sierra Leone's 10-year civil war, began in mid-2004.
Many RUF victims in the court sighed with relief at the verdicts. Sentences will be decided at a later date.
The BBC's Umaru Fofana at the court in Freetown said that as the verdicts were delivered, Sesay looked very serious and Kallon, clad in a smart light green suit, could have been mistaken for one of the lawyers, while Gbao buried his face in his hands and looked very dejected.
The last case to be held at the special court had heard how the rebel leaders were involved in the rape, mutilation and killings of civilians.
On Wednesday the judges concluded the rebel chiefs "significantly contributed" to a joint criminal enterprise with former Liberian President Charles Taylor to control the diamond fields of Sierra Leone to finance their warfare.
They were also found guilty of forced marriage - the enslavement that countless young girls suffered when their villages were raided and they were forced to "marry" a rebel.
The convictions mark the first time the forced marriage charge has been successfully handed down in an international court of law.
The trial heard harrowing tales from 75 prosecution witnesses of rapes and killings at the hands of the RUF.
The three rebels chiefs were initially indicted along with RUF founder Foday Sankoh, a close ally of Mr Taylor. But Sankoh died in custody before the case ever came to trial.
Tactics favoured by the rebels included amputating hands and arms or carving the initials RUF into the bodies of their victims.
The RUF was notorious for using the so-called Small Boys Units - child soldiers forcibly recruited and issued with AK-47 assault rifles - who had a reputation for particular cruelty among the civilian population.
By the time the conflict ended, some 120,000 people had been killed while tens of thousands were left mutilated, their arms, legs, noses or ears cut off.
Sierra Leone expert Gregory Gordon, a US law professor who has worked as a prosecutor in Africa, told the BBC's Network Africa programme: "When we think about blood diamonds, when we think about people having their hands chopped off, when we think about child soldiers and sexual slavery and forced marriages - all the horrors of the civil war in Sierra Leone, we think about the Revolutionary United Front."
The only trial still ongoing before the UN-backed Special Court for Sierra Leone is that of Mr Taylor, whose case has been moved to The Hague for security reasons.
He faces 11 counts of war crimes and crimes against humanity.
The Sierra Leone conflict was depicted in the 2006 film Blood Diamond, starring Djimon Hounsou, Leonardo DiCaprio and Jennifer Connelly.