Favre, also known as Peter Faber, was declared a saint by Francis on December 17th, the pope's 77th birthday, in an accelerated procedure which bypassed Vatican tradition and the canonisation ceremony, and without the confirmation of a performed miracle.
In his homily, the pontiff called on Jesuits to follow Favre in his "desire to change the world".
"Favre was utterly centred in God, and because of that he could go - obediently, and often on foot - all over Europe, to speak to all with sweetness, and announce the gospel," he said.
Favre, who lived from 1506 to 1546, was the first recruit of Jesuit founder St Ignatius Loyola.
A shepherd during his boyhood years, he later travelled to Paris to study, where he met Ignatius and another future Jesuit, Francis Xavier, both of whom had a huge influence on him spiritually.
He was ordained as a priest in 1534, and served across Europe, walking huge distances between religious postings in Germany, Spain and Portugal.
He was reportedly welcomed by his enemies as much as his friends. His remains are buried at the Church of the Gesu, the principle Jesuit church in Rome, where Friday's ceremony was held.
In an interview with the Jesuit journal La Civilta Cattolica last year, Francis praised the priest's ability to "dialogue with all, even the most remote and even with his opponents".
He said he admired Favre's "simple piety, a certain naivety perhaps. His being available straightaway, his careful interior discernment, the fact that he was a man capable of great and strong decisions but also capable of being so gentle and loving."
The pontiff entered Favre into the "catalogue of saints" through the rarely used "equivalent canonisation" process, whereby popes can declare universal veneration for someone who has enjoyed widespread reverence over a long period of time.