Addressing a sharply divided audience at the storied Catholic university, Obama nevertheless conceded that no matter how much Americans "may want to fudge it ... at some level the views of the two camps are irreconcilable."
"Each side will continue to make its case to the public with passion and conviction," he said. "But surely we can do so without reducing those with differing views to caricature."
The commencement ceremony was boycotted by a number of graduates dismayed by the university's decision both to tap Obama as its commencement speaker and to give him an honorary degree. The president is a supporter of abortion rights and federally-funded embryonic stem-cell research - positions that are anathema to traditional Catholic teachings.
Some graduates attended the ceremony, but expressed their disapproval by donning a mortar board marked with a cross and the outline of an infant's footprints. Others countered by wearing mortarboards adorned with an Obama campaign symbol.
Twenty-seven people were arrested prior to Obama's speech, according to a spokeswoman for the St. Joseph County, Indiana, jail. Norma McCorvey, the plaintiff identified as "Roe" in the 1973 Roe v. Wade Supreme Court decision, was among those arrested.
But inside, several hecklers who interrupted the start of Obama's speech were loudly booed by the audience.