Toua Udia, 22, denied touching the man inappropriately at Tesco on Dalmarnock Road in Rutherglen, South Lanarkshire, on July 21.
At the end of a two-day trial, Sheriff Martin Jones said he was not satisfied beyond reasonable doubt that the Crown had proved the case against Mr Udia, who is from Papua New Guinea, and acquitted him with a not proven verdict.
Speaking afterwards, Ian Moir, Mr Udia's lawyer, said: "Mr Udia has maintained his innocence throughout and is delighted with the outcome of the case.
"He now wishes to put this behind him and is looking forward to returning to see his family."
In evidence yesterday, Mr Udia's accuser told Glasgow Sheriff Court the athlete touched his testicles while he was helping him strap an ice pack to his leg.
Earlier this morning the court heard from Crown witness Graham Buchanan, a security guard at Tesco, who said a man came up to him in the store and told him a male athlete had touched him in the toilets.
He said the man seemed quite angry and pointed out Mr Udia, who was wearing a red tracksuit in his country's colours, bearing the name of his nation and his Commonwealth badge.
Mr Buchanan told the court Mr Udia looked "calm and relaxed" and his demeanour did not change when he told him there had been a complaint about him, and he remained "relaxed".
Procurator fiscal depute Adele MacDonald asked what Mr Udia's response was when told a man had made an allegation against him regarding an incident in the toilets.
Mr Buchanan said: "He seems to know that something happened but doesn't comment."
The security guard said Mr Udia later gave his own version of events.
He said: "He stated that in the toilet he was trying to tighten his bandage and another male was asked to help him and when he was helping, the accused's hand slipped and struck the gentleman."
The prosecutor urged Sheriff Jones to convict Mr Udia, saying the accuser was in no doubt that it was a deliberate act, and other witnesses had noted the complainer's anger afterwards.
In his closing submission, Mr Moir said: "The conduct of the accused is not eloquent of someone who has committed a sexual offence. The witnesses speak to him co-operating, and going about the store for quite some time."
He added: "He tells the security staff when they make him aware of why they want to speak to him that there was an accident and that he had apologised."
Sheriff Jones said the Crown have to prove the case against the accused beyond reasonable doubt.
He said: "Having regarded the evidence and all of the circumstances of this case, I am not satisfied that the Crown have proved the case against you and I acquit you on a verdict of not proven."