The episode has caused hilarity online but the Vatican says it is seeking an explanation from the Facebook-owned platform, alongside an investigation at the Holy See.
'We can exclude that the "like" came from the Holy See, and it has turned to Instagram for explanations,' a Vatican spokesperson told the Guardian.
Pope Francis's official Instagram account appears to have liked a racy photo of Brazilian model Natalia Garibotto (pictured), 27, showing her in a schoolgirl's uniform
The Pope's official account appears to be have been one of more than 133,000 to have liked the 27-year-old Brazilian model's picture
A screenshot taken by an eagle-eyed social media user shows the @francisus account liking the picture
Garibotto joked on Twitter after discovering what had happened: 'At least I'm going to heaven.'
She also linked to her website with the light-hearted caption: 'If Pope Francis wanted the site, so should you.'
The model's management company, Coy Co, also took advantage of the apparent error by declaring that Garibotto had 'received the pope's official blessing'.
'Legend has it, Pope Francis is subscribed to [her website] under a pseudonym,' they joked.
Francis's account does not follow anybody on Instagram, and papal social media is managed by a team of Vatican employees.
Vatican sources told the Catholic News Agency that an investigation was underway to determined what had happened.
The Brazilian model joked 'at least I'm going to heaven' after the social media mishap
The picture was originally posted on Garibotto's account in early October, but it was not clear exactly when the pontiff's 'like' appeared.
The apparent papal approval was rescinded on November 14 after the Vatican was alerted to the mistake.
The image showed Miss Garibotto dressed in a short tartan skirt while packing books into a locker and received more than 160,000 likes in addition to the misdirected one.