Jared Perry said in a release issued late Friday that he is stepping down to allow the student association to focus on remedying the damage done earlier this week when a video of the chant was circulated on social media.
"My stepping down allows the Association and its leaders to focus exclusively on the work of remediating the damage earlier this week to the reputation of the Association," he said in the release.
However, Perry also says in the release he intends to run as a candidate for the president's job in the next election.
He said he believes it's up to students to assess his leadership.
Perry has already apologized for being among the male and female orientation leaders who performed the chant to about 400 students assembled on the football field at the university on Labour Day as frosh week activities kicked off.
The song spells out the word "young'' with a comment after each letter and includes: ``Y is for your sister ... U is for underage, N is for no consent... .''
A video was posted on Instagram on Wednesday, causing fierce criticism both in Nova Scotia and across the country.
Perry has called the chant "a huge mistake," yet added it has been part of frosh events since at least 2009 when he sang it as his initiation, with the lyrics being put down on paper and passed to orientation leaders.
He couldn't explain why student leaders hadn't cancelled the chant in the past, but has said it has revealed "a problem of a culture of sexism" on the campus.
Criticism of Perry's leadership continued after the news conference, and a facebook page emerged lobbying for his resignation.
The student association news release says Carrigan Desjardins, the vice president of student life, also resigned. She was responsible for the student association's frosh week program.
Meanwhile, the university announced that two unnamed student organizers face possible disciplinary action over the chant.
Saint Mary's spokesman Steve Proctor said a complaint has been received that the student organizers violated the student code of conduct and the matter will be sent to a three-person disciplinary panel for a hearing.
Penalties for violating the code of conduct range from fines to suspensions to expulsion, said Proctor.
However, the process is private and names won't be revealed, he added.
Earlier on Friday, Saint Mary's University announced it has hired an outside expert to lead a task force on sexual violence.
University president Colin Dodds says Wayne MacKay, a law professor at Dalhousie University, will head up a council that will examine ways to create a "culture change" at the school's campus in Halifax.
The university says MacKay will look at methods to inspire respectful behaviour and a safe learning environment within Saint Mary's.
His group will produce recommendations by the middle of December.
MacKay, a former president and vice-chancellor of Mount Allison University, recently authored a report on preventing bullying and cyberbullying for the Nova Scotia government.
He has also served as the executive director of the Nova Scotia Human Rights Commission and the vice-chairman of the International Centre for Human Rights and Democracy.