Mr. Obama received a lengthy ovation from students and spectators when he walked onto the stage, and later when he was given an honorary Doctor of Laws degree, citing him for inspiring a healing of divisions of religion, culture, race and politics.
His commencement speech is expected to touch on the debate that has roiled the campus for weeks and divided many.
CBS News White House correspondent Mark Knoller reports that as his motorcade left the airport, about 100 friendly people waved at Mr. Obama from across the street, their banners reading "We Love Obama" and "We Support Our POTUS."
Knoller said Mr. Obama encountered no protesters as he entered the Joyce Center via the back way.
In recent days, protests over his appearance and the honorary degree to be conferred on him built to the point that police arrested 19 demonstrators Saturday and at least another five on Sunday.
Those arrested Sunday included Norma McCorvey, the plaintiff identified as "Roe" in the Roe v. Wade case that led to the Supreme Court decision legalizing abortion. She has since opposed abortion and was part of a 200-person protest at the university's gate.
"Shame on Notre Dame," read one sign at the university's gate. Another declared "Stop Abortion Now."
Some students at Mass wore T-shirts showing a leprechaun throwing a baby into a trash can. The shirts' back side read, "May 17, 2009, The day the dome was tarnished forever" and showed a drawing of the school's famed golden dome covered in blood.
In Washington on Sunday, the head of the Republican Party said Mr. Obama should be denied the honorary degree.
President Obama supports abortion rights but says the procedure should be rare. The Catholic Church and many other Christian denominations hold that abortion and the use of embryos for stem cell research amount to the destruction of human life and are morally wrong and should be banned by law.
The contrary argument holds that women have the right to terminate a pregnancy and that unused embryos created outside the womb for couples who cannot otherwise conceive should be available for stem cell research. Such research holds the promise of finding treatments for debilitating ailments.
Within weeks of taking office in January, President Obama eased an executive order by President George W. Bush that limited research to a small number of stem-cell strains.
White House spokesman Robert Gibbs said Friday that Mr. Obama in his commencement speech would mention the debate over abortion while emphasizing that "this is exactly the kind of give and take" that occurs on college campuses everywhere.
The Rev. John Jenkins, Notre Dame's president, has not joined the debate that erupted after Mr. Obama's invitation. Friends and colleagues say Jenkins has listened to the criticism but is confident in his decision.
"He respects people who differ, but he's resolute in his decision because he did it based on conscience and what he really believes in," said Richard Notebaert, chairman of Notre Dame's board of trustees.
Notebaert said Jenkins, who is in the fourth year of a five-year term, has the "full support" of the trustees.
That hasn't soothed critics, who question whether Notre Dame has lost touch with its Catholic roots. Calls for Jenkins' ouster have grown louder amid protests by abortion opponents, who have paraded dolls smeared in fake blood outside a recent trustees' meeting and on Sunday flew an anti-abortion banner over campus.
To be sure, though, there was division on campus, both among students and faculty.
Hundreds of students filled the campus' South Quad for an open-air Mass and rally during which the Rev. Kevin Russeau praised the students for responding to the controversy over Obama's invitation with prayer.
"I can't tell you the number of Rosaries and Masses and prayer meetings that have been intentional responses to what many feel is a concession to the culture of death," he told the worshippers.
The Rev. Richard McBrien, a theology professor at Notre Dame who supports Mr. Obama's speech, noted that the president's positions put him at odds with Catholic doctrine, but added: "There are other positions he has taken, whether it's on immigration or poverty or whatever, which are entirely consistent with Catholic social teaching."
McBrien appeared on "Fox News Sunday."