Paula Podest Ruiz, 39, and Carlos Ciuffardi Elorriga, 41, who had a civil union eight years ago, told the pope that a religious ceremony that was to follow was canceled after their parish church in Santiago was heavily damaged in an quake in 2010. "Here?" they replied, to which the pope responded "yes" and promptly married the happy couple.
The Pope was highlighting the conflict between the state and the Mapuche people, who centuries ago controlled vast areas of Chile but have since been marginalised.
The duo explained that while technically married, they had only been joined through a civil ceremony.
In an unprecedented moment, the Holy Father Pope Francis delivered the sacrament of marriage to two cabin crew members onboard LATAM flight LA1250 from Santiago to Iquique in Chile today. That we have two daughters and that we would have loved to receive his blessing.
The Vatican says this is the first time the pope has conducted a marriage ceremony midflight.
Pope Francis suggested performing the brief ceremony on his short flight from Santiago to the city of Iquique in northern Chile.
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"The day they bring me proof against Bishop Barros, then I will speak", the pope said in response to a journalist's question about the 61-year-old bishop, appointed by Francis in 2015 despite being accused of covering up another priest's abuse of boys.
They asked him to bless their marriage.
Pope Francis himself was struck by what appears to have been an item of clothing or a towel as he greeted crowds from the popemobile on his way to an open-air Mass in Chile's capital, Santiago.
"And that's why the marriage works", Ciuffardi said.
He said he knew the pain of priests and nuns "who after working so hard, have seen the harm that has led to suspicion and questioning; in some or many of you this has been a source of doubt, fear or lack of confidence". "Hopefully, this will motivate couples around the world to get married", Ciufardi said.
It all started when the pair, Paula Podest Ruiz and Carlos Ciuffardi Ellorriaga, began chatting with the pontiff when they were seated next to him during a group photo shoot.