Eric Breteau, who founded Zoe's Ark, and his partner Emilie Lelouch had been tried in absentia but appeared in the Paris court for Tuesday's verdict.
Four other members of the group were given suspended sentences of between six months and a year.
Zoe's Ark received a 100,000 euro (£86,000) fine and has been dissolved.
The children were said to have been orphans from Sudan's war-torn Darfur region, but turned out to be mainly from Chad and with families of their own.
In a case that shocked France, the defendants were arrested in Chad as they tried to load the children on to a plane bound for France in 2007.
They were sentenced later that year to eight years' hard labour by a court in the Chadian capital, N'Djamena, but repatriated to France after receiving a pardon from Chad's president in March 2008.'Any price'
The six defendants were charged, in France, with acting illegally as an adoption intermediary, facilitating illegal entry into France, and fraud in regard to 358 families who had expected to adopt children.
Four of the six defendants turned up for the trial in ParisMr Breteau and Ms Lelouch, who had been living in South Africa, refused to attend the start of the trial in early December, reportedly saying they had "no wish to give an account of themselves".
But they appeared in court on Tuesday to hear the judge rule that they should face a two-year prison sentence, a fine of 50,000 euros each and a ban on working with minors. Their lawyer said they would appeal.
The pair "could not have been unaware of the illegality of their project," the court said, adding that they had "knowingly lied to their families".
Of the other defendants, Dr Philippe van Winkelberg and Christophe Letien received a one-year suspended sentence, and Alain Peligat and journalist Marie-Agnes Peleran were each given six-month suspended terms, French media reports.
Mr Breteau, a former volunteer firefighter, set up Zoe's Ark in 2005, initially to aid victims of the December 2004 Asian tsunami.
In April 2007, the charity announced a campaign to evacuate 10,000 young orphans from Darfur in western Sudan, which was suffering a humanitarian crisis following five years of civil war. Zoe's Ark said it planned to place the children, all mainly under five years old, in foster care with French families.
However, the 103 children the charity was putting on to a plane from Chad to France in 2007 were found to be largely from Chad itself, and were not orphans at all.
The court heard damning testimony from Nathalie Cholin, a volunteer nurse who had provided psychological support to medical teams in Chad.
She portrayed Mr Breteau as an "all-powerful manipulator" who had convinced her at a meeting in Paris that his mission in Chad would rescue Darfur orphans find them homes in France.
Assurances were given, she said, that the operation was perfectly legal: "He told us we were acting under the 1951 Geneva Convention and I did not imagine an operation like this could be organised without the backing of the authorities."
However, once in Chad, Ms Cholin found the children were "in good health" and were "crying and asking to go back to where they had come from".
For Eric Breteau, "children had to be brought back at any price", she told the court, adding that she believed he was under "a certain pressure" from the families wishing to adopt the "orphans".
