In the federal suit, Paul Nungesser said he was cleared of responsibility in Emma Sulkowicz's 2013 rape claim, as well as others that came to light after Sulkowicz went public with her allegations in various media interviews.
Her case drew national attention after she started carrying a mattress around the Manhattan campus -- including her commencement ceremony -- to protest the school's handling of the complaint. She said hoped to show how "flawed" the university disciplinary system is when it comes to sexual misconduct cases.
CNN does not usually name individuals in sexual assault cases, but in this instance, both parties have spoken publicly about their experience.
The suit said Nungesser was found "not responsible" for "nonconsensual sexual intercourse" after Sulkowicz filed a complaint with Columbia's Office of Gender-Based Misconduct about the alleged assault in 2012.
On Friday, U.S. District Judge Gregory Woods dismissed Nungesser's Title IX suit, saying his claims do not constitute sex-based discrimination. The term "rapist" is not gender-based, he said.
"He assumes that because the allegations against him concerned a sexual act that everything that follows from it is 'sex-based' within the meaning of Title IX," the judge wrote. "He is wrong."
Woods added, "Taken to its logical extreme, Nungesser's position would lead to the conclusion that those who commit, or are accused of committing, sexual assault are a protected class under Title IX."
Woods also said the former student had not proven that the university deprived him of an education.
"The Court does not suggest that Nungesser's senior year at Columbia was pleasant or easy," Woods wrote in his opinion.
"Title IX, however, sets a high bar before a private plaintiff may recover and Nungesser has not alleged facts showing that he was effectively deprived of Columbia's educational opportunities."
In a statement released by their son's attorney, Karin and Andreas Nungesser said, "We all are disappointed by the decision of the court. But we look forward to taking on this opportunity that the court has given us to re-plead our case and amend the complaint.
"We still believe that it is untenable that the rule of law and the assumption of innocence ends behinds campus gates. If the court dismisses the amended complaint as well, all parents who are planning to send their sons to college should know: Innocent until proven guilty no longer applies on college campuses."
Nungesser has 30 days to submit an amended complaint before the dismissal is final.
The university said in a statement, "We are encouraged that today's ruling brings us closer to the point that this litigation, addressing issues understandably difficult for many, can be concluded," according to the student-run Columbia Spectator newspaper.
Nungesser, an international student from Germany, filed the suit last April, naming the school; its president, Lee Bollinger; and the visual arts professor who oversaw Sulkowicz's mattress project, "Carry That Weight," as part of her senior thesis.
He alleged the university violated his right to an education free of gender-based discrimination by allowing Sulkowicz to speak out against him after he had been cleared of wrongdoing. During an April 2014 news conference at Columbia University, Sen. Kirsten Gillibrand stood alongside Sulkowicz as she called Nungesser a "serial rapist" and said she feared for her safety while he was still on campus.
Bollinger also commented on the case in a 2014 New York Magazine profile of Sulkowicz, now a senior at Columbia.
"This is a person who is one of my students, and I care about all of my students. And when one of them feels that she has been a victim of mistreatment, I am affected by that. This is all very painful."
The case produced dueling narratives from both sides in national media outlets. In a Daily Beast article titled, "Columbia Student: I Didn't Rape Her," Nungesser shared a long exchange of Facebook messages to support his claim that their sex was consensual.
Some of those exchanges were included in the lawsuit, but Sulkowicz told CNN they were taken out of context in the suit.
She also balked at the idea that Nungesser would sue the school or her professor "for allowing me to make an art piece."
"It's ridiculous that he would read it as a 'bullying strategy,' especially given his continued public attempts to smear my reputation, when really it's just an artistic expression of the personal trauma I've experienced at Columbia," Sulkowicz wrote in an email. "If artists are not allowed to make art that reflects on our experiences, then how are we to heal?"
The project essentially consisted of Sulkowicz carrying a twin-size mattress wherever she went on campus.