The case, which was the result of complaints filed by two groups opposed to talks with Eta, was thrown out on Monday after prosecutors requested that the charges be dropped as meeting Batasuna members was not explictly prohibited by law.
The decision comes ahead of a March 1 regional election in which Ibarretxe's moderate Basque Nationalist Party (PNV) risks losing power to the Socialists, who are led by Patxi Lopez, one of the other people accused in the trial.
Mikel Casas, Ibarretxe's lawyer, surprised the court on Thursday by requesting that the trial continue to the end to obtain a ruling that proves his client "was right".
"We want to prove the innocence of the Lehendakari as well as that of the others. What they did, taking a step forward to search for peace, was fair and legitimate," he said using the Basque name for the head of the northern region's government.
The defendants faced possible prison terms and bans on political activity if they had been found guilty.
The cases against five Batasuna members, including Arnaldo Otegi, the group's leader, were also dismissed.