The remarks were first reported last week by The Associated Press, and Ohio State at the time called them unacceptable and said it had placed Gee on a "remediation plan" to change his behavior.
Gee, 69, said in a teleconference that the furor was only part of his decision to retire, which he said he had been considering for a while. He said his age and the start of a long-term planning process at the university were also factors.
"I live in turbulent times and I've had a lot of headwinds, and so almost every occasion, I have just moved on," he said. Gee explained away the abrupt timing by saying he was "quirky as hell" and hated long transitions.
He also said he didn't regret the way he conducted himself as a higher education leader.
"I have regrets when I have said things that I shouldn't have said, but I have no regrets about having a sense of humor and having a thick skin and enjoying life," Gee said.
According to a recording of a Dec. 5 meeting obtained by the AP under a public records request, Gee, a Mormon, said Notre Dame was never invited to join the Big Ten athletic conference because "you just can't trust those damn Catholics."
Gee also took shots at schools in the Southeastern Conference and the University of Louisville, according to the recording of the meeting of the school's Athletic Council.
Gee apologized when the comments were disclosed, saying they were "a poor attempt at humor and entirely inappropriate."
His decision to retire was first reported by The Columbus Dispatch.
Robert Schottenstein, who as chairman of the university's board of trustees condemned the remarks last week as "wholly unacceptable" and "not presidential in nature," deflected questions about whether Gee had been forced out by the board.
"It's really about a decision to retire for the reasons that Gordon has articulated," Schottenstein said.
Ohio State, one of the biggest universities in the nation, with 65,000 students, named provost Joseph Alutto as interim president.
Gee, a familiar figure on campus with his bowties and owlish eyeglasses, has repeatedly gotten in trouble over the years for verbal gaffes. Tuesday's news lit up Twitter, with numerous posts using the hashtag (hash)savethebowtie.
Ohio State trustees learned of Gee's latest remarks in January and created the remediation plan. In a March 11 letter, the trustees warned any repeat offenses could lead to his firing and ordered him to apologize to those he offended. But it appeared that several of Gee's apologies came only in the last week or so as the school prepared to respond to the AP's inquiries.
Gee said Tuesday he waited until recently to apologize in person to the Notre Dame president, Rev. John Jenkins, because they had a long-scheduled meeting. Schottenstein said the board was satisfied with Gee's response to the letter.
On Monday, Gee withdrew as Saturday's commencement speaker at a Catholic high school in Columbus, saying he wanted the focus to remain on the students.
In the recording of his meeting with the Athletic Council, Gee said that the top goal of Big Ten presidents is to "make certain that we have institutions of like-minded academic integrity. So you won't see us adding Louisville." After laughter from the audience, Gee added that the Big Ten wouldn't add the University of Kentucky, either.
When asked by a questioner how to respond to SEC fans who say the Big Ten can't count because it now has 14 members, Gee said: "You tell the SEC when they can learn to read and write, then they can figure out what we're doing."
Notre Dame and the SEC had no comment on Gee's retirement.
Gee also came under fire in 2011 for some offhand remarks he made during a scandal on football coach Jim Tressel's watch. Asked whether he had considered firing Tressel, Gee said: "No, are you kidding? Let me just be very clear: I'm just hopeful the coach doesn't dismiss me."
Tressel, later forced out by the university, said in a statement Tuesday it had been an honor to work with Gee.
Last year, Gee apologized for saying that coordinating the school's many divisions was like running the Polish army, a remark that a Polish-American group called bigoted.
In 1992, in a moment of frustration over higher-education funding, Gee referred to then-Gov. George Voinovich as "a damn dummy." Voinovich said Tuesday there were no hard feelings and he considered Gee one of his best friends.
Gee didn't edit himself much Tuesday during a teleconference announcing his retirement, joking about the imposition of "this damn telephone call."
"I've only got a month to ruin the university," he quipped. "I've got to get at it."
Gee was named the country's best college president in 2010 by Time magazine. He has held the top job at West Virginia University, the University of Colorado, Brown and Vanderbilt. He was Ohio State president from 1990 to 1997 and returned in 2007. He makes about $1.9 million a year in base pay, retirement benefits and other compensation.
He is a prolific fundraiser and is leading a $2.5 billion campaign at Ohio State. He is omnipresent on campus, attending everything from faculty awards events to dormitory pizza parties.
Allison Roda, 22, one of many Ohio State students stunned by the news, lamented she'd have to graduate without him.
"This is just so upsetting. He just represents everything great about college life," Roda, a fifth year senior from Broadview Heights in suburban Cleveland, said as she walked on Ohio State's giant green dubbed the "Oval." She said she is a Catholic who considered attending Notre Dame and she wasn't offended by Gee's remarks.
Gov. John Kasich praised Gee on Tuesday as "a tremendous partner in transforming Ohio's fragmented higher education system into one better focused on fueling Ohio's economic recovery and helping students meet their goals."
The president of the American Council on Education said Gee, who is a board member, left an "indelible mark" on each institution he served.
"He is an iconic leader, unparalleled in skills and widely respected among presidents, chancellors, policymakers and business leaders at both the state and federal levels," ACE President Molly Corbett Broad said in a statement.