The trio were released on bail on Wednesday after their embassy, which said Jordan's King Abdullah had taken a personal interest in the case, promised they would return to court to face trial.
"The International Paralympic Committee and LOCOG have been informed by the Jordanian National Paralympic Committee that three athletes released on bail following incidents in Northern Ireland will not be entered into the London 2012 Paralympic Games. The athletes have returned to Jordan," a statement said.
LOCOG are the London organisers for the August 29 - September 9 Paralympics.
The two wheelchair-bound power lifters and trainer were arrested on Monday and accused of sexual offences involving two women and two underage girls, the Northern Irish court heard.
Weightlifter Omar Sami Qaradhi was charged with three counts of sexual assault and one of voyeurism on Wednesday. Two of the alleged assaults were against children.
His colleague Motaz Al-Junad faced one sexual assault charge. Trainer Faisal Hammash was charged with two counts of causing a child to engage in sexual acts.
The 19-strong Jordanian squad was one of several from the Middle East and Africa training in Northern Ireland's Antrim Forum sports centre ahead of the London Games for disabled athletes, which comes just weeks after the Olympics in the city.
The court was told the alleged offences had taken place between August 16 and 20.