The comments - a portion of which were posted in a YouTube video - were "out of time, out of line, and out of character," Thomas said. "As a president of a university, you should not have those kinds of conversations with men or women."
Jennings, 63, who had led the historically black university since January 2012, did not return a call for comment.
His resignation took immediate effect, and the university's general counsel, Valerie Harrison, stepped in as acting president while Lincoln searches for a long-term interim leader and permanent replacement.
Harrison, who previously worked for Arcadia and Temple Universities, has been at Lincoln since 2013. The task force she announced will be composed of faculty, students, and staff. The campus also will invite experts on gender equity and sexual violence to address the university community, she said.
The campus has roiled since The Inquirer this month reported on Jennings' remarks to an auditorium filled with female students. A protest at the board of trustees' meeting on Nov. 15 drew about 100 students, parents, and alumni.
In his speech, Jennings said: "We have, we had, on this campus last semester three cases of young women who, after having done whatever they did with young men and then it didn't turn out the way they wanted it to turn out, guess what they did? They went to Public Safety and said, 'He raped me.' "
Jennings said such allegations can ruin a young man's life: "Don't put yourself in a situation that would cause you to be trying to explain something that really needs no explanation had you not put yourself in that situation."
He told The Inquirer he was referring to three cases in which women falsely reported rapes as revenge against men who had been unfaithful.
But Michael Noone, first assistant district attorney in Chester County, said he could find no evidence to back up the president's assertion.
During his September address, Jennings also advised female students about how men can deceive and exploit women, and how women have to protect themselves.
"Men treat you, treat women, the way women allow us to treat them. ... We will use you up if you allow us to use you up," he told them.
Then, he continued, those men will "marry the girl with the long dress on."
Jennings at first defended his remarks to The Inquirer, but days later apologized for his choice of words, saying, "I certainly did not intend to hurt or offend anyone."
His nearly three-year tenure had become increasingly rocky. Both faculty and alumni gave him votes of no confidence. Faculty members have expressed concern about dropping enrollment, lagging fund-raising, and high turnover in administrative posts.
On Monday, Harrison announced plans to form a faculty advisory council. She said meetings with students, staff, and alumni also would be held.
Harrison earned a bachelor's degree in economics at the University of Virginia, a juris doctorate from Villanova University School of Law, and a master's in liberal arts from Temple. She is due to receive her doctor of philosophy degree in African American studies from Temple next month.
"The parents are exceptionally gratified that this has come to a close, certainly before the end of the semester, certainly before the holiday break, so it can be peaceful," said Carmina Taylor, head of Lincoln's parents association. "It's been very cantankerous, very uncomfortable for the last few weeks. We have a renewed spirit and commitment to Lincoln University."
Parents in recent weeks submitted a complaint to the U.S. Department of Education, contending Lincoln has not complied with the Clery Act, a federal law that requires prompt and accurate reporting of campus crime.
Faculty members said they hope the university can move forward positively.
"We've taken a beating," said Robert Langley, a chemistry professor and president of the faculty union. "It appears as if the university isn't sensitive toward its student population. And we have some of the most sympathetic people. They very much adore the students. That's the real image. We just have to make sure we move on and put Lincoln in a positive light."
Late Monday afternoon, the campus was nearly empty. Students left on Friday for Thanksgiving break.
Kristen Houser, a spokeswoman for the Pennsylvania Coalition Against Rape, said Lincoln - as have some other universities that have faced adversity over their handling of sexual assault - should use the controversy as a way "to examine what gaps they really have, do some self-reflection, and seek out assistance to make it better."
"I would certainly hope as they search for new leadership, they are asking about sensitivity to these issues," she said.
Inquirer staff writer Kelly Flynn contributed to this article.