The justice ministry said Eric Breteau, the head of Zoe's Ark, and his girlfriend left a prison south of Paris by a side door to escape journalists at the main gate.
Zoe's Ark, the French charity, had sought to fly 103 children to France for adoption after claiming they were orphans or refugees from Sudan's war-wracked Darfur region.
Breteau and five colleagues were sentenced on December 26 to eight years hard labour, before being sent to France to serve equivalent sentences in jail.
The Zoe's Ark members were detained on October 25 as they were about to put the children on a French-bound flight from the main eastern Chad town of Abeche, across the border from Darfur.
International aid staff later found almost all the children to be Chadian and to have at least one living parent.
A second decree issued by Deby on Monday pardoned local intermediary Mahamat Dagot, a community chief from the Chadian town of Tine, near the Sudanese border.
Dagot had been convicted last year of "complicity in the attempted kidnap of children" and sentenced to four years of hard labour.
Souleimane Ibrahim Adam - a Sudanese refugee who worked with Zoe's Ark as an intermediary and who, like Dagot, faced four years in prison with hard labour - had not received a pardon because he had not yet asked for one, Padacke said.
The Zoe's Ark case raised tensions between France and Chad, a former French colony, as Paris prepared to spearhead a 3,700-strong EU peacekeeping force in eastern Chad to protect refugee camps in the region bordering Darfur.
A vanguard of the 14-nation mission deployed to Chad and the Central African Republic (CAR) last month.
In Paris, on Monday, the lawyer for Nadia Merimi, one of the detained, hailed the pardon, saying: "I just learned this news with pleasure and relief. Wisdom has prevailed."
|"I just learned this news with pleasure and relief. Wisdom has prevailed"|
Lawyer for one of the aid workers
He said Merini would try to restart her career following her release.
Celine Lorenzon, a lawyer for Breteau, said the six had been in prison too long and added Breteau "can't take it anymore".
The six were repatriated in accordance with a bilateral agreement once the Chadian courts agreed. As hard labour does not exist in France, they were only jailed.
After months in an orphanage, the first wave of children caught up in the adoption scandal returned home earlier this month to their tearful parents, accompanied by Chadian and United Nations officials.
Wrangling over the damages and interest of $9.8m that the Chadian court ordered Zoe's Ark to pay on December 26 is continuing.
The French government, which supported Deby when rebels attacked the Chadian capital in February, welcomed news that a presidential pardon was on the cards, but refused to pay the money owed to the families.
"It is not for the government to pay, but at the same time, a solution must be found," Bernard Kouchner, the foreign minister, said at the time.
Seven Spanish flight crew, three French journalists and a Belgian arrested along with the six French charity workers back in October were freed last year and allowed to return to Europe.