The 62-year-old Qatari is serving a lifetime ban from football after being accused by FIFA of bribery during his failed bid to become the world governing body's president in May.
As the most senior AFC member, China's Zhang Jilong assumed the roles of acting head and FIFA Executive Committee member after the ban.
Bin Hammam was attempting to overturn that decision and be reinstated to both roles in the interim ahead of his CAS hearing into the FIFA ban and the AFC decision.
Bin Hammam had ran against FIFA President Sepp Blatter but withdrew from the race on May 29 after being accused of handing $40,000 bribes in brown envelopes as a sweetener to Caribbean football officials to secure their vote.
Blatter was re-elected unopposed for a fourth term three days later.
Bin Hammam, who was re-elected unopposed for a third and final term as AFC head in January, has continually said he was innocent and is taking his case to CAS after having his appeal against the decision rejected by FIFA last month.
The Qatari has been heavily critical of FIFA since the decision in May.
He has appeared to flout FIFA rules on the ban from all football by using AFC headed paper and referred to himself as the AFC president when making public a number of statements on his blog.
The AFC said they welcomed the decision by CAS to reject the appeal to have Zhang removed.
"AFC has strictly followed the AFC Statutes at all times in relation to Mr Jilong's designation as AFC Acting President and nomination to the FIFA Executive Committee," the statement read on Monday.
"Hence, AFC welcomes the CAS decision on provisional measures and is confident of its prospects of success at the CAS hearing on the merits of the appeal."
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