"It has been my privilege to serve as President of this remarkable institution. It has been an honor to work with our faculty, students, staff, alumni, and community members to advance Penn's vital missions," said Magill in a statement.
Magill will remain a tenured faculty member at Penn Carey Law. Plans for interim leadership at Penn would be shared in the coming days.
Penn Board of Trustees Chair Scott L. Bok also announced his resignation Saturday evening, a spokesperson told ABC News.
In a statement first reported by Penn's student newspaper, the Daily Pennsylvanian, Bok said, "Today, following the resignation of the University of Pennsylvania's President and related Board of Trustee meetings, I submitted my resignation as Chair of the University's Board of Trustees, effective immediately."
Bok said he had been asked to remain in his role to help with the presidential transition but believed "now was the right time to depart."
He called Magill "a very good person and a talented leader" and "not the slightest bit antisemitic."
"The world should know that Liz Magill is a very good person and a talented leader who was beloved by her team. She is not the slightest bit antisemitic," Bok wrote. "Working with her was one of the great pleasures of my life. Worn down by months of relentless external attacks, she was not herself last Tuesday," said Bok in the statement.
Magill faced a rebellion from the leaders of the university's prominent Wharton School, and a growing coalition of donors, politicians and business leaders who denounced her testimony.
She had already been under fire from prominent donors, faculty, students and alumni prior to Tuesday's hearing after multiple incidents of antisemitism on campus in recent months - and what critics have said was a tepid response to those incidents.
Magill became Penn's ninth president on July 1, 2022 after serving as executive vice president and provost at the University of Virginia. Prior to that she was the Richard E. Lang Professor and Dean of the Stanford Law School.
During Tuesday's House hearing, Magill, along with the presidents of Harvard and MIT, did not explicitly say that calling for the genocide of Jews would necessarily violate their code of conduct on bullying or harassment. Instead, they explained it would depend on the circumstances and conduct.
WATCH | Penn president testifies to House Education Committee about antisemitism on campus
New York Republican Rep. Elise Stefanik asked Magill to respond "yes or no" if calling for the "genocide of Jews" violated Penn's rules or code of conduct.
Magill replied, "If the speech turns into conduct, it can be harassment. Yes."
Stefanik followed up: "I am asking, specifically, calling for the genocide of Jews, does that constitute bullying or harassment?"
Magill responded that it was a "context-dependent decision."
"It's a context-dependent decision -- that's your testimony today?" Stefanik countered. "Calling for the genocide of Jews is depending upon the context?"
WATCH | Rep. Elise Stefanik grills Penn, Harvard presidents about antisemitism on campus
After the fallout from Tuesday's hearing, Magill attempted to clarify her message on Wednesday, posting a video on X where the Penn leader said she should have focused on 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."
Magill said that Penn's policies "need to be clarified and evaluated," adding that in her view: "It would be harassment or intimidation."
On Saturday, Bok said Magill was exhausted and made a misstep - but she was unfairly treated.
"Worn down by months of relentless external attacks, she was not herself last Tuesday," Bok said. "Over prepared and over lawyered given the hostile forum and high stakes, she provided a legalistic answer to a moral question, and that was wrong. It made for a dreadful 30-second sound bite in what was more than five hours of testimony."
The House Education and Workforce Committee launched an investigation with full subpoena power into Harvard, MIT and the University of Pennsylvania, Republican Rep. Elise Stefanik announced Thursday afternoon.
Several of Pennsylvania's elected leaders denounced Magill's comments, including Gov. Josh Shapiro, who condemned Magill's testimony as "shameful."
"That was an unacceptable statement from the president of Penn," Shapiro, who is Jewish, said Wednesday. "Frankly, I thought her comments were absolutely shameful. It should not be hard to condemn genocide."
Shapiro said if calling for the genocide of Jews "doesn't violate the policies of Penn, well, there's something wrong with the policies of Penn that the board needs to get on, or there's a failure of leadership from the president, or both."
Shapiro is a nonvoting board member at the university.
White House spokesman Andrew Bates issued a statement Wednesday criticizing all three university presidents who testified, saying their responses did not go far enough to condemn antisemitism on campuses.
"It's unbelievable that this needs to be said: calls for genocide are monstrous and antithetical to everything we represent as a country," he said.
A petition on Change.org demanding Magill's resignation had more than 26,000 signatures as of Saturday afternoon.
Despite its name, Penn is a private school and is not run by the state.
University Board of Trustees Chairman Scott Bok full resignation statement:
"Today I submitted my resignation as Chair of the University of Pennsylvania Board of Trustees, effective immediately. While I was asked to remain in that role for the remainder of my term in order to help with the presidential transition, I concluded that, for me, now was the right time to depart.
Former President Liz Magill last week made a very unfortunate misstep-consistent with that of two peer university leaders sitting alongside her-after five hours of aggressive questioning before a Congressional committee. Following that, it became clear that her position was no longer tenable, and she and I concurrently decided that it was time for her to exit.
The world should know that Liz Magill is a very good person and a talented leader who was beloved by her team. She is not the slightest bit antisemitic. Working with her was one of the great pleasures of my life. Worn down by months of relentless external attacks, she was not herself last Tuesday. Over prepared and over lawyered given the hostile forum and high stakes, she provided a legalistic answer to a moral question, and that made for a dreadful 30-second sound bite in what was more than five hours of testimony.
I wish Liz well in her future endeavors. I believe that in the fullness of time people will come to view the story of her presidency at Penn very differently than they do today. I hope that some fine university will in due course be wise enough to give her a second chance, in a more supportive community, to lead. I equally hope that, after a well deserved break, she wants that role.
I likewise wish my innumerable friends across the Penn campus well as they forge ahead in this challenging time."
ABC News and CNN contributed to this report.