The prosecution rejected the choice of witnesses and asked the court to disregard the defence's request.
Monday was supposed to be the first day of witnesses called by the defence, with Gbagbo's lawyers calling figures including parliament speaker Guillaume Soro, former premier Jeannot Kouadio Ahoussou and former army chief Philippe Mangou.
"We are suspending our participation until further notice. The process is biased, the court does not want a fair trial," said Dohora Blede, one of the lawyers defending Gbagbo over post-election violence that left more than 3,000 dead in 2010-11.
"We noticed that our witnesses were not present -- we have asked for a delay of four days to see these people, who are indispensable for demonstrating the truth."
The prosecution rejected the choice of witnesses and asked the court to disregard the defence's request, which it did after two hours of deliberation, saying it did not have the authority to call them.
"We are stunned -- these people include some who have gone to the International Criminal Court (ICC) thousands of miles away. We're asking them simply to come here by car. We can't explain it," the defence lawyer said.
Gbagbo has been on trial since the end of May, accused of involvement in the shelling of Abobo, a northern suburb of Abidjan which was a stronghold of Alassane Ouattara, who beat her husband Laurent in the 2010 election and is now president.
She is also accused of involvement in the bloody repression of women in Abobo, and of participating in a "crisis cell" which coordinated pro-Gbagbo attacks by the armed forces and militias.
She is already serving a 20-year sentence for "endangering state security".
Ivory Coast, the world's top cocoa producer, was rocked by deadly violence for five months after Laurent Gbagbo refused to concede the 2010 election to Ouattara.
Laurent Gbagbo is currently on trial before the ICC in The Hague.