The vote of 141-93 with 10 abstentions allowed Shamseddin Hosseini to remain in his post, Iran's Press TV reported Wednesday.
During a heated question-and-answer session, Hosseini denied any involvement in the case but accepted responsibility and apologized to the Iranian people.
"I did not resign my post because this $2.6 billion financial fraud case occurred during my tenure, and I had to make up for it," he said.
Hosseini told lawmakers he tried to implement fundamental reforms, the Tehran Times reported.
Iranian President Mahmoud Ahmadinejad defended Hosseini's performance.
Two dozen people have been arrested and 67 others have been questioned in the bank fraud case, Iran's top prosecutor said.