The mother, Clara Rojas, had argued allowing the film "Operation E" to be shown in Colombian theaters would harm the development of her son, Emmanuel, who is now 9.
But Judge Raquel Aya said, in a brief description of her decision posted to the Bogota court's website on Wednesday night, that the film does "not violate the child's basic rights."
The court said Rojas, a 49-year-old attorney, was appealing the decision.
She could not immediately be reached for comment and declined to discuss the case after a court hearing Wednesday.
Rojas' attempt to bar the film's release in Colombia was criticized by anti-censorship advocates, including writers, film critics and even President Juan Manuel Santos.
One of the film's producers, Farruco Castroman of Spain's Zirco Zine, said it will likely be released in Colombia in March.
Emmanuel's story, a heart-tugging tale from the depths of Colombia's long civil conflict, has enthralled a nation that was particularly traumatized by rebel kidnappings in the 1990s and 2000s.
Rojas was campaign manager for presidential candidate Ingrid Betancourt in 2002 when the two were seized by the Revolutionary Armed Forces of Colombia, known as the FARC.
Rojas conceived Emmanuel with a rebel she has not identified and his arm was injured during a difficult cesarean section in the jungle. In 2004, rebels took the boy, then age 7 months, from his mother and the two were not reunited until the FARC released her three years later.
The film focuses on Jose Crisanto Gomez, the poor farmer to whom rebels initially delivered the boy. Rojas objected to that, saying Gomez held her son "captive" for seven months before turning him over the Colombia's child welfare agency.
The actor who plays Gomez in the film, Luis Tosar, won best-actor award for the performance last year at the Biarritz, France, film festival.
The Spanish and French filmmakers say they were intrigued by Gomez's story because he claimed not to have known until Rojas' release that the fair-skinned baby was born to a political hostage.
Officials doubted that claim, initially protecting Gomez then prosecuting him.
The government put him in a witness protection program in late 2007 after the FARC came to him demanding he return the baby. But in May 2008, four months after Rojas was freed, he was jailed on charges including kidnapping, rebellion and giving false testimony.
In April, he was freed, having never been tried, though the chief prosecutor's office is appealing Gomez's release.
Gomez, 44, denies any association with the FARC, saying they were simply "the authority" in the area, where he grew coca, the basis for cocaine.
Gomez, a father of seven who has been looking for work after losing his farm and saw his marriage fall apart, earned an undisclosed sum to serve as an adviser for the film, even while he was still in prison, said Castroman.
And last year, he spent three months in Europe at screenings of the film, including at the San Sebastian festival in Spain.
Castroman said the filmmakers tried to negotiate with Rojas and offered her 1 percent of box offices receipts in Colombia.
He said she wanted 1 percent of global receipts.
Associated Press Writer Cesar Garcia contributed to this report.