Ben Brik had originally been sentenced on November 28 last year on charges of physically assaulting and insulting a 28-year-old businesswoman, Rym Nasraoui, after a traffic accident.
Two witnesses were cited but neither they nor Nasraoui ever gave evidence in court. Ben Brik was not present Saturday when the sentence was confirmed for "voluntary assault, damage to property and breach of good morals".
Ben Brik, 49, had protested his innocence throughout his trial last year, arguing he was the victim of a set-up by police because of his criticism of Ben Ali, elected in October for a fifth term after two decades in power.
He said he was arrested two hours after "the publication of an imaginary interview" with the president at the time when he was seeking re-election.
The decision "confirmed the total absence of independence in the Tunisian justice system", Ben Brik's lawyer William Bourdon said in a statement Saturday.
Ben Brik, currently detained in Siliana prison, 130 kilometres (80 miles) from Tunis, will remain there unless he receives a presidential pardon or appeals to the supreme court in the next ten days.
It is "state terrorism", his wife Azza Zarrad said. "Once again we have a decision made by the state, not justice".
"To top it all off, this state is supported by European members of parliament who talk up the economic success of Tunisia and it is presented as a barrier against terrorism", she added.
Zarrad said she would take the case to the United Nations.
Rym Nasraoui's lawyer had rejected the claims that she had been manipulated by police and said she had no relationship with politics.
Ben Brik's lawyers stressed that their client had not been given the opportunity to confront the plaintiff nor the two witnesses.
France has also expressed regret at Ben Brik's imprisonment, saying it highlighted the difficulties hampering journalists and human rights defenders in Tunisia.
The French foreign ministry and the European parliament in Strasbourg both welcomed Azza Zarrad recently, whilst there have been a number of calls in France for President Nicolas Sarkozy to intervene.
Media rights group Reporters Sans Frontieres (RSF - Reporters Without Borders) has declared Ben Brik a political prisoner and said Saturday it was "disappointed" by the appeal court decision.
"Nothing justifies" Ben Brik staying in prison, RSF said.
"We hoped the judges would have shown more independence" the group's secretary general Jean-Francois Juillard said in a statement, "the prosecution file is empty".
"Now we must ensure that Taoufik's conditions of detention are as good as possible".
Ben Brik suffers from Cushing's syndrome, a disease that threatens the immune system and requires medical monitoring and a clean and warm environment.
Another Tunisian woman has also accused the journalist of "violence" in an incident in France, another "trap" according to Ben Brik's French lawyers.
Ben Brik is the author of satirical writings targeting the Tunisian president in the French media.
His nine books and his articles have not been published in Tunisia, where he is unknown to the general public and, if mentioned in the local press, is usually called a "villain", "alcoholic" or "traitor".
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