The 24-year-old had been accused of withholding commission on multi-million pound deals brokered by sports management firm Proactive, who used to represent him.
Rooney made no payments after soccer agent Paul Stretford, a director and founder of Proactive, left the firm in acrimony in October 2008, taking with him their top client.
Rooney, who is currently on holiday in Barbados after a miserable World Cup campaign in South Africa where he failed to score, was signed by Stretford for Proactive in 2002.
Rooney, then 17, went from a trainee with Everton to a household name, attracting lucrative sponsorship deals with the likes of Nike and Coca-Cola.
Proactive had argued that, as such contracts for Rooney and his wife Coleen were brokered by Stretford while he was still at the firm, they were still due the 20 per cent commission -- amounting to £4.3 million.
However Judge Brendan Hegarty, who had postponed his ruling at Manchester Mercantile Court until after the World Cup, said the original contract Rooney signed with Proactive amounted to a "restraint of trade" as it was up to eight years long when the Football Association recommended a maximum of two years.
He said Proactive was only entitled to a "restitutional remedy" from Rooney amounting to around £90,000, the Press Association reported.
"I am delighted to have won this case," the striker said in a statement.
"Coleen and I have always been happy to pay all commissions due to the people who were owed them.
"But these sums were a joke and we felt they were just an attempt to exploit us. Fortunately the judge has knocked back their massively over-inflated claims and we are happy to pay the very small sum awarded," he added.
Proactive's lawyer Ian Mill told the court they would consider taking the matter to the Court of Appeal.
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