Justice Wylie acknowledged the assessment he made about Mrs Banks was "an error" and asked the former MP to pass on his apologies to his wife.
The judge would also make reference to it in his final written decision, he told the court.
Speaking to the Herald after the hearing, Mr Banks said it was "a historic day".
"Justice Wylie's comments were indeed reassuring and comforting for Amanda. I've spoken to her - she's thankful and she's grateful," he said.
"She's such an honest traveller so to have the judge say those things today was a great step of redemption for her. It was a giant leap of redemption."
It is a rare step for a judge to make such a public acknowledgment and Mr Banks said his lawyer David Jones, QC, had told him he had never seen anything like it during his long legal career.
Mr Jones told the court today his client had suffered a "grave injustice" and was "seeking justice for a level of recompense for costs incurred in this court".
The lawyer said the Crown exhibited a "blinkered approach" in terms of the prosecution and made reference to "perjured evidence".
"Clearly the evidence was false by Mr Dotcom, Mrs Dotcom and indeed [Dotcom's former bodyguard Wayne] Tempero. It can't have been true," Jones said.
But John Billington, QC, for the Crown, rejected those claims.
"There was no evidence available to the Crown that suggested what was being said by Mr Dotcom, Mrs Dotcom and Mr Tempero was fabricated. On the contrary, the other evidence supported it," he said.
Mr Banks took aim at the Crown for what he said was a campaign to blacken his name.
"What we do know is the Crown were vindictive, obstructive and in the end blatantly dishonest," he said.
"They became fixated with their hell-bent commitment to destroy me."
After 37 trips to court, Justice Wylie's impending decision on costs will be the final chapter in the long-running saga.
Though it had taken it out of the ex-Act MP, he said he would always fight to clear his name.
"I didn't spend a lifetime and work in politics doing the wrong thing and I knew that in the end justice and common sense and redemption would follow, but it's been a long haul," he said.
"When your reputation is challenged you have to throw everything at it to put it right. I was never going to go away."
The original case related to donations Mr Banks received from Dotcom for his 2010 Auckland mayoral campaign that were not disclosed on his electoral return and which he claimed were anonymous.
The Court of Appeal quashed his conviction after Mrs Banks' leg work.
In March, Mr Banks was awarded $66,200 in costs from the Crown for the Court of Appeal hearings that resulted in his acquittal.