The Confession program has gone on sale through iTunes for £1.19 ($1.99).
Described as "the perfect aid for every penitent", it offers users tips and guidelines to help them with the sacrament.
Now senior church officials in both the UK and US have given it their seal of approval, in what is thought to be a first.
The app takes users through the sacrament - in which Catholics admit their wrongdoings - and allows them to keep track of their sins.
It also allows them to examine their conscience based on personalised factors such as age, sex and marital status - but it is not intended to replace traditional confession entirely.
Instead, it encourages users to understand their actions and then visit their priest for absolution.
"Our desire is to invite Catholics to engage in their faith through digital technology," Patrick Leinen of developer Little iApps told Reuters.
The launch comes shortly after Pope Benedict XVI gave urging to Christians to embrace digital communication and make their presence felt online.
In his World Communications Address on 24 January, he said it was not a sin to use social networking sites - and particularly encouraged young Catholics to share important information with each other online.
"I invite young people above all to make good use of their presence in the digital world," he said.
He warned them to keep in mind that digital communication was part of a bigger picture, however.
"It is important always to remember that virtual contact cannot and must not take the place of direct human contact with people at every level of our lives."
The app guides users through different elements of the sacrament
Confession's developers, who are based in Indiana, said they took the Pope's words to heart when they were preparing the application for public consumption.
"Our goal with this project is to offer a digital application that is truly 'new media at the service of the word'," said the company.
The firm said the app was developed with assistance from several priests and had been given the church's imprimatur by Bishop Kevin Rhoades of the Diocese of Fort Wayne in Indiana.
A spokesperson from the Catholic Bishops' Conference of England and Wales told BBC News the app was a "useful tool to help people prepare for the Sacrament of Reconciliation".
"The Church believes in embracing new technology and this creative app will hopefully help people to make a good confession."
It is thought to be the first time the church has approved a mobile phone application, although it is not entirely unfamiliar with the digital world.
In 2007, the Vatican launched its own YouTube channel.
Two years later created a Facebook application that lets users send virtual postcards featuring the pontiff.
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