Archbishop Thomas Wenski led a small delegation of Miami-area priests to Wednesday's ceremony, The Miami Herald reported.
"It demonstrates that there is a future for a church that serves as a witness of hope, which is what Cuba needs in this moment," Wenski said before his departure.
The seminary 10 miles from Havana is proof of a changing relationship between the Castro regime and the church. Pope John Paul II blessed the first stone for the complex when he visited Cuba in 1998, although construction did not begin in earnest until 2006.
The seminary's predecessor was converted to a military barracks by the government in 1966.