Vatican newspaper, L'Osservatore Romano, reports that the pope welcomed Fr Tom at his residence on 13th September.
It said Fr Tom knelt before the pope and kissed his feet. The newspaper also said Pope Francis was emotionally moved by the gesture, and helped the priest up and kissed his hands.
Pope Francis gave Fr Tom a blessing and said he would continue to pray for him as he did during his abduction.
According to the paper, Fr Tom thanked the Pope said "he prayed every day for him, offering his suffering for his mission and the good of the church."
Fr Tom was kidnapped in March 2016 when gunmen destroyed a care home he was serving at run by nuns in the capital Aden. Four nuns and 12 others were murdered in the attack.
According to Oman's Ministry of Information, Omani authorities had played a role in securing Fr Tom Uzhunnalil's release, through liaison with parties in Yemen.
Pope Francis has previously appealed for the release of Fr Tom.
