Usher will remain the primary legal guardian of his two young sons.
The 34-year-old R&B singer shares Usher V, five, and Navivyd Ely, four, with his ex-wife Tameka Foster.
Usher Jr. almost died on Monday after nearly drowning in the pool at his father's Atlanta, Georgia home.
Tameka filed legal papers to have an emergency custody hearing shortly after the incident. In the documents she reportedly asked for "temporary primary custody of their two children".
The court addressed the issue during a hearing on Friday in which both Usher and Tameka were present.
Usher, the star's aunt Rena Oden and Tameka gave hours of emotional testimony in court. Tameka claimed Usher was a negligent and unresponsive father who often put the care of their children into someone else's hands. Usher contended he was not an absentee parent and that he never once attempted to bar Tameka from their children's lives.
After hearing the sworn statements, the judge ordained the current custodial order should remain in place and the magistrate dismissed Tameka's case.
Usher walked up to Tameka, hugged her and reportedly whispered "I'm sorry" into her ear after proceedings were over. He then embraced his aunt in a celebratory fashion.
Contract workers at the residence are credited with freeing Usher Jr. and giving him CPR after he reportedly got stuck in the pool drain while trying to get a toy. His aunt was looking after him at the time of the incident.
Usher Jr. is said to be recovering well.
Usher divorced Tameka in 2009 after almost two years of marriage and a contentious custody battle ensued for years until the musician won primary legal guardianship in August 2012.