Two other defendants - former university professor Vincent Ntezimana and former Transport Minister Alphonse Higaniro - were also found guilty.
The Rwandan nuns were found guilty of homicide on Friday.
Two men accused of helping plan and carry out the killings received 20 years and 12 years respectively.
The prosecution in the war crimes trial had called for all four defendants to receive life sentences.
They were being tried for their complicity in the 13-week genocide in 1994 that resulted in the death of 800,000 Tutsis and moderate Hutus.
Rwanda's Government welcomed the guilty verdict.
"It is highly positive that Belgium, a foreign country, pursues and punishes crimes against humanity committed in Rwanda," Rwandan Justice Minister Jean de Dieu Mucyo told the Reuters news agency.
A lawyer for the victims of the genocide also expressed his satisfaction with the convictions.
"We are obviously very satisfied. I think the jury's verdict is balanced, even if it might seem severe on the whole for the four defendants, of course. So it is balanced and it recognises, I think, everybody's guilt," said the lawyer, Eric Gilet.
Landmark trial
The 12 jury members reached their decision after deliberating into the early hours of Friday morning. They are the first civilians to have judged war crimes suspects from another country.
The court heard how the two nuns handed over thousands of people who had sought refuge in their convent.
They even supplied cans of petrol to the Hutu militias, who set fire to a garage sheltering some 500 refugees.
Two other defendants - former university professor Vincent Ntezimana and former Transport Minister Alphonse
Higaniro - were also found guilty.
The Belgian trial took place outside the United Nations Rwanda tribunal process in Arusha, Tanzania.
It was the first time Belgium had used a law passed seven years ago, allowing its courts to hear cases of alleged human rights violations even if they were committed abroad.
The court heard how the two nuns enthusiastically embraced genocide when they handed over up to 7,000 Tutsis sheltering in the convent in southern Rwanda.
Survivors' testimony
In the two months that the trial has lasted, the jury has heard evidence from many survivors of the Rwandan genocide.
The defendants, who all now live in Belgium, had maintained their innocence throughout the trial. Their lawyers claimed they were the victims of a conspiracy.
Human-rights groups hope the trial will set a precedent and make it harder for war criminals to seek sanctuary abroad.
Belgium is the former colonial power in Rwanda, and its willingness to stage the trial may come in part from concerns here that it did not do enough to stop the genocide.