Billionaire investor John Paulson won a major victory in his bitter fight with a former business partner after an arbitrator ordered about $48 million paid back to him and concluded he was justified in firing one of his top executives.

The decision, revealed Monday, is the latest twist in Paulson’s long-running feud with Fahad Ghaffar, a former top aide who helped run Paulson’s Puerto Rico empire before the men fell out with each other.

An arbitrator found that Ghaffar engaged in “intentional misconduct and fraud” and was properly terminated by Paulson in July 2023, according to a filing submitted Monday in federal court in Puerto Rico.

Ghaffar was ordered to pay back $35.66 million in profits tied to an investment known as Dynamic Payments and repay another $112,936 connected to American Express rewards points that the arbitrator found were improperly retained.

Carolyn Demarest, the retired New York judge who was serving as the arbitrator, also found that Ghaffar committed fraud in connection with Paulson’s $11.48 million investment in software company Innoveo, according to a court filing.

All told, Ghaffar owes Paulson about $48 million, under the arbitrator’s decision.

“Following a three-week hearing, the Arbitrator ruled that Mr. Paulson proved, by clear and convincing evidence, that Ghaffar was terminated for Cause, finding that Ghaffar committed fraud, securities fraud, and violated both his fiduciary and contractual obligations to Mr. Paulson,” Paulson’s lawyer said in a statement to The Post.

Paulson, who made billions betting against the housing market before the 2008 financial crisis, first hired Ghaffar in 2013 to help oversee a growing portfolio of hotels, resorts and real estate investments on the island.

The relationship eventually deteriorated into an ugly courtroom battle.

In 2023, Ghaffar sued Paulson, claiming the billionaire reneged on a deal that would have given him a 50% stake in F40, a luxury car dealership venture in Puerto Rico.

Ghaffar alleged he invested roughly $17 million into the business with the understanding it would convert into a 50% equity stake.

Months later, Paulson fired back with a racketeering lawsuit accusing Ghaffar of siphoning millions of dollars from company accounts to fund a lavish lifestyle.

The latest arbitration ruling stems from a separate dispute over compensation and profit-sharing arrangements between the men.

After a three-week hearing that concluded last November, Demarest found that Ghaffar misled Paulson about his financial interest in Innoveo while arranging contracts between Paulson-controlled companies and the software firm that boosted Innoveo’s value.

The arbitrator concluded that Ghaffar’s conduct amounted to deception, fraud and securities fraud and provided grounds for termination under the parties’ agreement.

“Respondents have proved, by clear and convincing evidence, that Claimant committed acts of intentional misconduct or fraud,” Demarest wrote.

The ruling also found that Ghaffar improperly took for himself an opportunity to invest in Dynamic Payments after advising Paulson to pass on the deal.

While Demarest said that conduct did not itself justify firing Ghaffar years later, she ruled that he breached his fiduciary duties and must surrender the profits he earned from the investment.

The arbitrator was less receptive to many of Paulson’s other allegations.

Demarest found that numerous claims involving furniture purchases, artwork, discounts, travel expenses and other alleged perks did not establish fraud or intentional misconduct under the demanding standard required to justify termination.

The case is not over.

In a follow-up order issued June 8, Demarest said additional damages issues remain unresolved and will be addressed in a second phase of the arbitration.

The Post has sought comment from Ghaffar’s attorney, Martin Russo.