Swiss businessman Hans-Dieter Cleven claimed the German former world number one owed him 40 million Swiss francs ($41.4 million, 36.5 million euros), after Becker was declared bankrupt by a court in London last month.
A tribunal in the Swiss city of Zug threw out Cleven's claim and ordered him to pay legal costs plus 90,000 Swiss francs in damages to the six-time Grand Slam winner, the ATS news agency reported.
Cleven, who said Becker had missed several deadlines to repay him the money without specifying the origin of the sum, can appeal against the ruling.
The 49-year-old Becker, currently working as a television pundit during the Wimbledon championship -- which he won three times as a player -- worked with Cleven on several projects in the past, particularly in the 1990s.
Becker has denied he is bankrupt and told the German press he can meet all his financial obligations.