She had previously made statements suggesting there was State involvement in the murder.
Mr Justice Cian Ferriter also ordered Ms O'Doherty to pay legal costs which are understood to run to a five-figure sum.
Ms O'Doherty sued Mr Guerin, an independent councillor and brother of murdered journalist Veronica Guerin, over comments he made at a Fingal Co Council meeting on September 10, 2018.
She had previously made statements suggesting there was State involvement in the murder. She was due at the council meeting to seek a nomination from Fingal councillors so she could run for the office of President of Ireland.
While she did not attend, Mr Guerin, in his speech to the meeting, rejected her suggestion of State involvement and criticised her for what she had said. The content of his speech was reported in the media.
A year later, she issued proceedings against Mr Guerin claiming he had defamed her in that speech. He denied the claims.
However, she had issued her proceedings a day outside the one-year time limit for bringing defamation cases and had not sought an extension of that time period. She did not sue any of the media outlets over their reports of his speech, the court heard.
As a result, on Tuesday, Ronan Lupton SC, instructed by Zoe Mollaghan of Flynn O'Driscoll Solicitors, asked the court to strike out her case under the Statute of Limitations. It was also argued her action was frivolous, vexatious, bound to fail or an abuse of process.
In emails to Mr Guerin's solicitor in the last few days, she said she did not intend to contest the dismissal application and she consented to it being struck out with no order as to costs.
The solicitors wrote back saying she must first agree to pay Mr Guerin's cost before a strike out on consent would be agreed but she refused to do so. She said it was her former solicitors, KRW of Belfast, who "erred in certain matters, rendering the action untenable through no fault of my own"
She also reiterated her view that she was not accepting that her action was in any way frivolous, bound to fail, or an abuse of process. "I remind you that perjury is a criminal offence", she wrote.
When the case came before Mr Justice Ferriter for hearing on Tuesday, he was told there was no appearance by or on behalf of Ms O'Doherty. The judge was also provided with the email exchange over the last few days.
The judge said that, under court rules, if Ms O'Doherty seeks a discontinuance of the proceedings, a notice must be served in writing and that had not been done.
The rules also provide that there must be consent from the defendant for a discontinuance with no order as to costs and there was no such consent here, he said.
In those circumstances, and having reviewed the papers and submissions from Mr Guerin's side, he was satisfied to grant a formal order striking out the case. It seemed to him the proceedings were bound to fail because there was simply no answer to the Statute of Limitations issue.
As Mr Guerin was successful in his application, he was also entitled to his costs, the judge said.