The winger's involvement on Spurs' on-going tour of the United States came as a surprise after he was ruled out of the Olympics with a back injury.
FIFA boss Sepp Blatter had suggested Bale could be banned if there was a complaint from the British team but a statement from Tottenham says the decision to omit the Wales international was made jointly with Stuart Pearce and his staff.
The statement read: "The club considers the recent comment and accusations regarding Gareth Bale's fitness to be wholly unacceptable and unjustified.
"For the avoidance of any doubt - Gareth sustained an injury as he built up his fitness ahead of joining up with Stuart Pearce's side. MRI scan reports were sent to the FA medical team on 29 June.
"He was subsequently not selected on the basis of this injury and the inability to predict recovery time. This decision was not taken lightly and made only after consultation with Team GB's medical team, who were in agreement.
"At no time was Gareth made unavailable for selection. We trust that this statement now clarifies this matter once and for all."