McInnes, who was 86, served as Fairfield U.'s president from 1964 to 1973. He had been a Jesuit priest for 52 years.
The university's facilities, enrollment and academic programming all expanded during his tenure.
Fairfield established the School of Nursing, the Graduate School of Corporate and Political Communication, and a new Center for Lifetime Learning, along with expanding the Graduate School of Education.
Bannow Science Center opened with computer equipment, along with the Nyselius Library, a multi-purpose campus center, four new residence halls and a central utility complex.
And the school's undergraduate enrollment grew from 1,290 to 2,500 students.
Fairfield, which had been founded as an all-male school, in 1970 began admitting women. Efforts also were made to recruit a more diverse student body; a new academic council gave the faculty more say in university affairs, and the lay advisory board of trustees merged with the board of Jesuit trustees, according to the university officials.
The university was not immune to the turbulence sweeping across the nation's campuses during that era. At one point, Fairfield students staged a 10-day strike and occupied two administration buildings.Under McInnes, Fairfield University played a role in a legal battle over the right of church-related colleges to receive federal aid under the "Higher Education Facilities Act of 1963."
With a legal team headed by Edward Bennett Williams, Fairfield joined three other Catholic colleges and universities in the state, winning their case at federal court in New Haven. An appeal to the U.S. Supreme Court was denied. The decision had long-range implications for the more than 600 church-related colleges and universities in the country.
McInnes said of the decision, the justices had "recognized religious pluralism and academic integrity as being compatible." The court, he said, "has not taken down the wall of separation of church and state. It has, rather, shown more clearly where the wall really is."
"We stand on the shoulders of those who come before us and we are greatly indebted to Father McInnes for the tremendous growth and innovation he brought to this campus," the Rev. Jeffrey von Arx, S.J., the current university president, said in a statement. "During a time of great social unrest, he addressed challenging issues and through his inspiring and indefatigable leadership led this university to new heights of academic achievement and social awareness.
"We are saddened by his passing, but so grateful for the generous life he lived here and throughout his entire ministry."
He promoted the university's involvement in a range of social and community programs throughout the region, including a joint program with Action for Bridgeport Community Development that led to establishment of the Upward Bound program at the school, student volunteer tutoring, the Big Brother and Big Sister programs, and local programs to support the Glenmary Home Missioners in Appalachia.
McInnes became president of the University of San Francisco after leaving Fairfield U., serving until 1977. He then served as president of the Association of Jesuit Colleges and Universities from 1977 to 1989. He was parochial vicar at St. Thomas Aquinas Parish at the University of Connecticut in Storrs from 1990 to 1997. McInnes spent his later years at Boston College, where he served on the faculty from 1997 to 2008.
He is survived by a niece, Tina Watson.
A wake will be held at Campion Center in Weston, Mass., from 3 to 5 p.m. Monday, with a 4:30 p.m. prayer service. A wake will also be held at St. Mary's Hall at Boston College from 7 to 9 p.m.
The funeral Mass will take place at 10 a.m. Tuesday in St. Ignatius Church at Boston College. Burial will be in Campion Center Cemetery.