The 24-year-old England player 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 football agent Paul Stretford, a director and founder of Proactive, left the firm in acrimony in October 2008, taking with him their top client.
Judge Brendan Hegarty said the contract Rooney signed with Proactive in 2002 was a "restraint of trade" as it was up to eight years long when the FA recommended a maximum of two years.
He said Proactive was entitled to a "restitutional remedy" from Rooney of around 90,000 pounds, the Press Association reported.
"I am delighted to have won this case," the striker, who is on holiday in Barbados after a miserable World Cup campaign in South Africa where he failed to score, said in a statement.
"(My wife) 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."
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