The three activists left the women's prison in Manouba, northeast Tunisia, in a police van just before midnight taking them to an interior ministry office for the final formalities for their release, according to an AFP journalist at the scene.
One of their lawyers, Souhaib Bahri, said the three women, who had been detained for a month, would fly back to Europe on Thursday morning.
Earlier on Wednesday the three militant feminists received suspended sentences of four months and one day after apologising for their protest action.
"It is a great joy to have spoken for the freedom of Femen in Tunisia and to have been heard," the defendants' two French lawyers Patrick Klugman and Ivan Terel told AFP.
The three were arrested outside the main courthouse in Tunis on May 29 while making a topless protest in support of Amina Sboui, a detained Tunisian activist with the same group.
They were jailed on June 12, originally with custodial sentences, for indecency and an attack on public morals, sentences criticised as harsh by international rights groups and European countries.
Sboui had been arrested for painting the word "Femen" on a wall near a cemetery in the central city of Kairouan last month, in protest against a planned gathering of radical Salafists. She risks prison terms of two years and six months respectively for desecrating a cemetery and indecency.
The initial appeal was adjourned last week to allow Islamist groups angered by the topless protest to contest the court's decision to reject their request to participate in the trial as a civil party.
On the eve of Wednesday's hearing, three topless feminist activists in Brussels jumped on visiting Tunisian Prime Minister Ali Larayedh's car, demanding their jailed comrades in the North African country be released.
During the appeal hearing the three women apologised for the first time for their actions and promised not to repeat the protest.
German Josephine Markmann earlier said to the judge, who had told her Muslim law prohibited such behaviour: "I regret this act and I apologise."
"We didn't expect to shock Tunisians to this extent. It is out of the question that we would do it again," said Pauline Hillier, one of the two French women also appealing against a four-month prison sentence for their demonstration last month.
The head of the Femen movement in Paris, Inna Shevchenko, admitted the apologies were an "unexpected turnaround of the situation", but said she had "suspicions that the activists have suffered enormous psychological pressures".
The three women had appeared at the court of appeal in Tunis dressed in the traditional Tunisian veil, or safsari.
Lawyers for a number of Islamist groups angered by the protest, who were seeking to participate in the trial as a civil party, criticised the short time it took to organise the appeal hearing and asked for another delay, which the judge refused.
One of them, Seifeddine Makhouf, denounced the "exceptional pressures on the prosecutor to arrange the hearing in the shortest time possible".
But Klugman accused the Islamists of trying to prevent the case from ever being resolved, and argued that there was nothing sexual about the women's protest.
"You cannot pervert the message of Femen. Their breasts were visible to the public but they were carrying a message you can't ignore. Stop looking at their breasts... and listen to them," Klugman told the court.
He added that the women believed they would be safe staging their protest "in a country that has just risen up for freedom".
The women's lawyers said they were still concerned that Sboui remained in detention.
"We aren't forgetting her and we will not let her languish," they said.
The release of the Femen three comes ahead of a planned visit by French President Francois Hollande early next month.