Sheikh Ahmad, a key Bach ally and head of the Olympic Council of Asia, won the support of the general assembly of the umbrella body for National Olympic Committees to postpone his re-election as president on Wednesday.
Bach said in a keynote address to ANOC delegates on Thursday that the Kuwaiti's decision to step aside had been the right move for the Olympic movement.
"We have said, first of all, that we respect the decision he took under his own will and we recognise that this decision, his decision, was taken in the interests of all of us," the International Olympic Committee president said.
"But we have also stated, at the same time, stepping aside temporarily cannot be interpreted as any admission of guilt and that the presumption of innocence has to prevail."
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Sheikh Ahmad has not specified what the case in the Swiss court entails but has proclaimed his innocence and on Wednesday said it was nothing to do with "sport or corruption".
Fijian Robin Mitchell, ANOC's senior vice-president, will head up the organisation in Sheikh Ahmad's absence but it is clear that the popular leader expects to return to his previous roles once the case is concluded.
Bach also said he hoped to see Sheikh Ahmad return soon.
"I would once more pay respect to Shaikh Ahmad Al-Sabah ... and the example he is setting by taking this responsibility to protect all of us," Bach added in a speech that was met with thunderous applause from delegates.
"We hope we can see him back here very soon after his case is solved. We will pay this respect then also on his hopeful return among all of you and among all of us."
(Reporting by Jack Tarrant, editing by Nick Mulvenney)
