Luis Rubio was arrested for improper conduct and sexual abuse of minors when he was in charge of a Las Cabras school in 2013.
A year later, the archdiocese of Rancagua dismissed him from his duties while an investigation was underway, with the results sent to the Vatican, which has now expelled him.
Rubio's case was brought to the forefront in May when a television report revealed an alleged network of sexual abuse carried out by a group of religious figures collectively known as "The Family."
Rubio was interviewed in the report, during which he admitted he had "made a mistake, but not committed a crime."
A total of 14 priests and other religious figures were suspended as the Church investigated the network, while Rancagua prosecutors also opened their own investigation.
Pope Francis in May accepted the resignation of five Chilean bishops amid accusations of abuse and related cover-ups. Meanwhile last week, prominent priest Oscar Munoz was arrested over allegations of sexual abuse and rape of at least seven children.
The pontiff also accepted the resignation of auxillary bishop Juan Jose Pineda in Honduras, who has faced allegations by former seminarians of sexual misconduct, the Vatican announced.
Pineda has given up his post as auxiliary bishop of the Catholic Church's archdiocese of Tegucigalpa, the Honduran capital, the Vatican said in a brief statement.
In March, former seminarians had accused the 57-year-old cleric of "serious sexual misconduct," according to the US weekly National Catholic Register.
The alleged incidents happened earlier this decade when Pineda was teaching at the archdiocese's seminary for those studying for the priesthood.
Pineda was considered the righthand man of Honduran Cardinal Oscar Maradiaga, one of the closest advisors to Pope Francis and head of the "C9", a council of cardinals who assist the pontiff in reforming the Vatican.