Ms Magill had sparked anger among alumni, students and donors when she declined to explicitly say that calling for the genocide of Jews would violate the Ivy League college’s code of conduct on bullying or harassment at a hearing on Tuesday.
Her appearance alongside the presidents of Harvard and the Massachusetts Institute of Technology (MIT), who also refused to denounce calls for genocide, set off a crisis which saw donors threaten to pull $100m in funding.
Scott Bok, the chair of UPenn’s board of trustees, announced Ms Magill had voluntarily tendered her resignation in a statement on Saturday.
In a separate statement, Mr Bok said he had also resigned with immediate effect on Saturday.
Calls for Ms Magill to quit had gathered momentum throughout the week, with UPenn’s Wharton School board of advisers writing to her in a letter on Wednesday that the university “requires new leadership with immediate effect”.
“In light of your testimony yesterday before Congress, we demand the university clarify its position regarding any call for harm to any group of people immediately, change any policies that allow such conduct with immediate effect, and discipline any offenders expeditiously,” the letter said.
There have also been growing calls for Harvard president Claudine Gay and Sally Kornbluth, the president of MIT, to step down after Tuesday’s controversial hearing before the House education and workforce committee.
Clips from the hearing quickly went viral showing New York Republican Congresswoman Elise Stefanik grilling the university leaders.
In a series of heated questions, Ms Stefanik asked whether student protesters who said the phrases “intifada” or “from the river to the sea, Palestine will be free,” would qualify as violating the universities’ code of conduct on bullying and harassment.
Ms Magill told the hearing that it was “context-dependent”.
She later backtracked on her comments in a video posted on X, saying she should have countered the “irrefutable fact that a call for genocide of Jewish people is a call for some of the most terrible violence human beings can perpetrate”.
In a statement, Mr Bok said Ms Magill would remain in the role until an interim president was appointed. She will retain her position as a tenured member at Penn Carey Law School, he said.
“On behalf of the entire Penn community, I want to thank President Magill for her service to the university as president and wish her well,” he wrote.
Ms Magill said in the statement that it had been a privilege to serve as UPenn president.
“It has been an honour to work with our faculty, students, staff, alumni, and community members to advance Penn’s vital missions,” the statement read.
Ms Gay has also apologised for her statements before the select committee in an interview with The Harvard Crimson.
“When words amplify distress and pain, I don’t know how you could feel anything but regret,” Ms Gay told the publication.
In a post on X on Saturday, Ms Stefanik wrote: “One down. Two to go.”
“This is only the very beginning of addressing the pervasive rot of antisemitism that has destroyed the most ‘prestigious’ higher education institutions in America,” she said.
There has been a dramatic increase of antisemitic and Islamaphobic hate crimes in the US since Hamas terrorists killed approximately 1,200 Israelis in surprise attacks on 7 October.
An intense bombing campaign and ground invasion of Gaza by Israeli forces has killed more than 17,000 Palestinians, according to the Gaza health ministry.