Wu's position was challenged by the AIBA's executive committee, who claimed the Taiwanese had led the sport to the brink of bankruptcy.
An AIBA statement announced that the Lausanne court's verdict confirmed Wu as amateur boxing's president.
Wu's executive committee had passed a motion of no- confidence against his leadership and had turned to Swiss courts in July to approve a temporary administration, accusing the president of financial mismanagement.
But that bid for urgent provisional control of the AIBA was rejected, with Monday's ruling also coming down in favour of the organisation's current boss.
But Wu has insisted the body is financially healthy, accusing his detractors of mounting "a military coup".
In its statement after the ruling the AIBA announced: "The Court decision upholds the position of AIBA President Dr Ching-Kuo Wu and Executive Director Mr William Louis-Marie to validly represent AIBA and to continue to work in the best interests of boxing...