In a telephone interview, Gillespie said that while he was disappointed in the complaints about his leadership, they did not play a significant role in his decision to leave. Gillespie, 63, said he made his decision in consultation with his Jesuit superiors.
He acknowledged that "at times, we could have done a better job responding to concerns," and said he intended to be more proactive in responding and communicating with faculty and students in the year ahead.
A university official said that the school was no longer running a shortfall, but now had a $7 million surplus.
"The move will undoubtedly help," said Randall Miller, a history professor, citing the faculty's loss of confidence in Gillespie's leadership. "This will provide opportunity and hope that we will be able to recover that sense of community and common trust that for so long was the St. Joe's way."
A university spokesman said Gillespie's decision to leave was mutual.
The Jesuit-run university has faced budget shortfalls over the last several years and has cut staff.
Gillespie's team also was criticized for a plan to accept as many as 1,500 freshmen this fall - 225 more than the year before - as a way to bring in more revenue. That move would have made the school appear less selective.
That plan did not materialize after faculty and students protested vigorously against it, and this year's freshman class will have 1,370 students when classes begin Aug. 25.
Even before that, there was tension at the 8,860-student Catholic university, which straddles the Philadelphia-Lower Merion border. More than a year ago, consultants found a campus where "suspicion and mistrust abound."
The university plans to conduct a search for a new president during the coming academic year.
The faculty senate also took a vote of no confidence in Louis J. Mayer, vice president of financial affairs. A university spokesman said Mayer would remain in his job.