Both were stripped of their priesthood "as a outcome of overt acts of abuse against minors".
Defrocking, officially called being "reduced to the lay state", is the harshest punishment the Church can inflict on a member of the clergy and such action has rarely been taken against bishops.
Recently, Cox was once again accused of committing sexual abuse in Germany.
Pope to canonize 20th Century icons Oscar Romero, Paul VI
The United Nations commemorates the anniversary of his death each year. Other soldiers are also mentioned as perpetrators of the murder.
Fernandez then retired and has been living in Peru.
Now 85 and reportedly in poor health, the prelate has lived at the institute since 2002, Ms San Martin said.
Legal proceedings were initiated in Germany against Cox over the alleged abuse of a child in care in 2004, Deutsche Welle radio reported.
Pope Francis has already apologized repeatedly to Chileans over the scandal, admitting the church failed "to listen and react" to the allegations, but vowed to "restore justice".
Last month Francis defrocked Father Fernando Karadima, an 88-year-old Chilean priest who was accused of sexually abusing teenage boys over many years.
In May, the Argentine pontiff accepted the resignation of five Chilean bishops amid accusations of abuse and related coverups.