The man was the focus of outrage this week when he said his bride's family fooled him into paying a $20,000 dowry but then took their daughter back. The commission said the two fought and she ran away, back to her family.
In Saudi Arabia, no law stipulates a minimum age for marriage. There's been a push for that in recent years, but extremely conservative religious scholars have pushed back.
After learning of the marriage, the commission sent an investigator to the girl's home in Al-Hurath village in Jizan province, in southwestern Saudi Arabia near the border with Yemen.
Dr. Hadi Al-Yami, who runs the commission's branch that covers that area, told CNN that the group sent an investigator to a courthouse where the man had complained to a local official.
The commission then reached out to the girl's family, offering legal help, Al-Yami said.
On Wednesday, Dr. Bandar Alaiban, the commission's president, said a meeting had taken place with the parents, man and the girl.
"A divorce has taken place," Alaiban told CNN, "and the dispute has now been resolved amicably."
The marriage angered human rights groups and activists.
Dr. Suhaila Zein al-Abedin of the Saudi National Association for Human Rights -- also a government-backed group -- voiced concern not only about the age difference, but the circumstances of the marriage.
"When you consider the very large difference in age, it looks more like this was not a marriage, but like the girl was sold," al-Abedin said. "The girl's parents need to be held responsible for this."
Prominent Egyptian activist Mona Eltahawy tweeted, "It's only when there's enough public outrage that we can fight #childmarriage. We are not angry enough to help that 15 y/o & others like her."