"We are all Catholics and believe in the same God". The Pope himself is criticised for appointing Juan Barros as Bishop of Santiago despite him facing accusations of covering up the abuse.
Fernandez said the devices used in the church attacks were crude and homemade.
History's first Latin American pope didn't refer by name to Chile's most notorious pedophile priest, the Rev. Fernando Karadima, who was sanctioned in 2011 by the Vatican to a lifetime of "penance and prayer" for sexually molesting minors.
A Chilean court later found the allegations against Fr Karadima to be truthful but said he could not be prosecuted because too much time had passed.
The Pope told participants, including a dozen Nobel peace laureates that "International relations can not be held captive to military force, mutual intimidation, and the parading of stockpiles of arms".
While in Santiago, Pope Francis is planning to hold an outdoor Mass for more than 500,000 people.
The leader of the world's 1.2 billion Roman Catholics also met Muslim refugees in Myanmar and Bangladesh a year ago and called for decisive action to solve political problems that cause many to flee.
"Sadly when we asked the Pope to remove Bishop Juan Barros, instead of helping us, he accused us of being stupid and left-wing and that is why we are here", she explains.
At least six churches have been bombed in three days, and one threat said the next bomb will be in Pope Francis's cassock.
"Yes, we hope to see Francisco someday in Argentina", said Dahiana Veroitza, 19, part of a contingent from southern Argentina attending the Mass. Mr Cruz, who was abused by Fr Karadima when he was a young boy, is adamant that "the time for saying sorry and forgiving is over".
However, Espinoza, who also appreciated Pope Francis' statements, noted that he expects more actions by the Vatican.
"There are concrete things that he can do, like removing priests who have been accused and sentenced by the Chilean justice system or canon law and bishops who have covered up [sexual abuse]", he says.
Since 2000, almost 80 members of the Chilean clergy have been accused of sexual abuse of minors, with more than half of the accused convicted by a Vatican court.
On Tuesday, the Pope will visit the Women's Penitentiary Center on the outskirts of Santiago, and later he will meet with priests, religious people and seminarians at the Metropolitan Cathedral. "And I wanted to share it with you", added Francis illustrating the picture as a "fruit of war".
Last week, the AP broke a story that the Vatican was so concerned about the Karadima scandal that it planned to ask three Chilean bishops to step down.
The Vatican spokesman, Greg Burke, has said that the Church has the utmost respect for those planning to protest against sexual abuse in the Church.
One abuse survivor said Francis's talk of "pain and shame" was not enough.