"A sword has pierced the heart of our city," the bishop said in a statement.
"The healing power of Jesus goes beyond our physical wounds but touches every level of our humanity: physical, emotional, social, spiritual," he said. "Jesus calls us to remain fervent in our protection of life and human dignity and to pray unceasingly for peace in our world."
The shooting rampage at a crowded nightclub in Orlando left 50 people dead, including the gunman, and 53 wounded.
Police said a lone gunman — identified as 29-year-old Omar Mir Seddique Mateen — opened fire inside the Pulse club in Orlando in the early morning hours. News reports said that Mateen, who pledged allegiance to the Islamic State terrorist group, died in a gun battle with SWAT team members.
Across the nation, reaction from Church and community leaders was swift, and in cities large and small, people organized candlelit vigils for the victims and their families the night of the shooting.
"Waking up to the unspeakable violence in Orlando reminds us of how precious human life is," said Archbishop Joseph Kurtz, president of the U.S. Conference of Catholic Bishops.
"Our prayers are with the victims, their families and all those affected by this terrible act," he said in a statement June 12. "The merciful love of Christ calls us to solidarity with the suffering and to ever greater resolve in protecting the life and dignity of every person."
"Our prayers and hearts are with the victims of the mass shooting in Orlando, their families and our gay and lesbian brothers and sisters," said Chicago Archbishop Blase Cupich.
In Orlando, priests, deacons and counselors from the Diocese of Orlando and Catholic Charities of Central Florida were serving at an aid centre established by city officials.
Throughout the day June 12, Church personnel were helping victims and families "on the front lines of this tragedy," Noonan said. "They are offering God's love and mercy to those who are facing unimaginable sorrow. They will remain vigilant and responsive to the needs of our hurting brothers and sisters."
The bishop also asked all parishes in the nine-county diocese in central Florida to include prayer intentions during Sunday Masses.
"Today's prayers have been offered for victims of violence and acts of terror ... for their families and friends ... and all those affected by such acts against God's love," Noonan said. "We pray for the people of the city of Orlando that God's mercy and love will be upon us as we seek healing and consolation."
Noonan planned to lead an evening prayer vigil for the community — called a "Vigil to Dry Tears" — at St. James Cathedral in Orlando June 13.
He said the Catholic Church "recognizes the affliction brought to our city, our families and our friends" by "this massive assault on the dignity of human life. ... I hope this opportunity to join each other in prayer will bring about an outpouring of the mercy of God within the heart of our community."
In his statement, Cupich expressed gratitude to the first responders and civilians at the scene of the shooting. They "heroically put themselves in harm's way, providing an enduring reminder of what compassion and bravery look like — even in the face of such horror and danger," he said.
"In response to hatred, we are called to sow love," he added. "In response to violence, peace. And, in response to intolerance, tolerance."