Ganczarski and Naouar are charged with complicity in the murders, and complicity in attempted murder, and face life sentences if convicted.
Both deny involvement in the attack.
Because two of those killed in the blast were French, the country's law means that a trial can be held in France.
French investigators say Nizar Naouar, 24, called Mohammed by satellite telephone in Pakistan and received the order to attack on the day of the bombing.
The prosecution claims that Naouar also contacted Ganczarski, and phone taps by German police indicate that the suicide bomber sought his blessing for the attack.
Nizar Naouar's body was never found.
Prosecutors also allege Ganczarski was in contact with senior al-Qaeda officials, including Osama bin Laden, during trips to Afghanistan and worked with the network as a computer expert.
Prosecutors say they suspect that Walid Naouar knew an attack was planned and bought the satellite telephone that was found in his brother's home and allegedly used for the calls to Pakistan and Germany.
As he entered the special court in the French capital, Stéphane Bono, Ganczarski's lawyer, said his client would not be facing a fair trial.
Bono said: "Christian Ganczarski is more afraid by injustice than by the justice system.
"He's been waiting for his trial for a long time, he has no religious authority to give orders or advice, he's someone who speaks Arabic very poorly, someone who only knows the prayers and greeting words.
"So it's useless and impossible to think that he's an executive for al-Qaeda... that's what President Sarkozy said at the national assembly when he was interior minister.
"That is why today I am asking for this case to be dropped as there has been an blatant breach of presumption of innocence and therefore it is impossible to have a fair trial."
Five Tunisians were also killed in the blast and 30 people were wounded.