Nathan Jacobson, the self-described “radioactive” businessman close to senior Conservatives, cleared his name Monday in a San Diego courtroom.

Justice Janis L. Sammartino accepted a deal reached between federal prosecutors and Mr. Jacobson’s lawyer, Mike Attanasio, allowing Mr. Jacobson to withdraw his 2008 guilty plea for money laundering in connection with an online pharmacy.

“I am thankful to the judge and the U.S. Justice Department for agreeing that the interests of justice required that my plea be withdrawn and all charges against me dismissed,” Mr. Jacobson said in an emailed statement. “It has been a long and difficult road to vindication. I look forward to returning to my family, my business, and my community involvement upon my return to Toronto. Today, justice was served.”

The ruling brings an end to a two-year nightmare for Mr. Jacobson, who moved in Canada’s top political, business and philanthropic circles until 2012, when he failed to show up for a sentencing hearing in San Diego and the Americans began an extradition process.

Mr. Jacobson, 57, was raised in modest circumstances in Winnipeg, served in the Israeli military and went on to make millions in Iraq, Russia and Israel.

After he pleaded guilty to clearing millions in credit card payments for an illegal online pharmacy, he was expected to serve three or four years in federal prison.

But after his extradition, he hired Mr. Attanasio and launched a legal process seeking to withdraw his guilty plea on the grounds that his previous lawyers, including Toronto lawyer Steven Skurka, had mishandled his case.

“Based on the evidence before this court, including Mr. Jacobson’s sworn declaration and the testimony of his former counsel, Steven Skurka, and the government’s non-opposition to the Motion to Withdraw, and good cause appearing, the court finds that there are fair and just reasons for withdrawal of Mr. Jacobson’s guilty plea. Accordingly, the court hereby grants the motion to withdraw, declares the plea agreement null and void, and vacates Mr. Jacobson’s guilty plea.”

Mr. Skurka’s lawyer, Brian Greenspan, who previously described Mr. Jacobson’s complaints about his client as ungrounded, was not immediately available for comment Monday.

“When we started working with Nathan, it became clear that he had repeatedly proclaimed his innocence before and after his guilty plea,” said Mr. Attanasio.

Sources familiar with the litigation said federal prosecutors felt that the agreement was a good idea, given the probationary sentences given to other defendants, the harm that Mr. Jacobson had already suffered, and cost and risk of continued litigation.

“It is always important when deciding an individual’s fate, to make sure you strike an appropriate balance,” lead prosecutor Philip Halpern said Monday. “In this case, when we examine the probationary sentences of the last six defendants against all that has happened to Mr. Jacobson, we believe this resolution is in the interests of both fairness and justice.”

Until his legal problems became public, Mr. Jacobson was friendly with senior cabinet ministers John Baird and Jason Kenney, as well as world leaders, including Israeli Prime Minister Benjamin Netanyahu and Russian President Vladimir Putin.

Mr. Jacobson, who has  Canadian and Israeli passports, has contacts with intelligence agencies going back decades and has been photographed with  Stephen Harper and Syrian President Bashar Assad.

Spokespeople for Mr. Baird, Mr. Kenney and Mr. Harper have said that they were not aware of Mr. Jacobson’s legal problems until they were reported in the summer of 2012.

Just hours before he was arrested by Toronto police, Mr. Jacobson told CBC News he had avoided contact with his political friends during his ordeal.

“I myself made the decision that it’s best to keep a distance, in order to protect my friends. I would for the most part consider them still my friends. But while I’m — for the lack of a better term — radioactive, better let them to continue to run government.”

In 2011, Mr. Jacobson sued York Centre Conservative MP Mark Adler, claiming that Mr. Adler had failed to pay him back more than $100,000 he invested in Mr. Adler’s Economic Club of Canada. Mr. Adler eventually settled the lawsuit, reportedly under pressure from Nigel Wright, then Mr. Harper’s chief of staff.