The president was at the church, about 9km from here, for around 20 minutes before heading to the Mangueshi Temple, located around 5 km away from there.
The body of the saint, who died in 1552, is encased in a silver casket and placed in a glass container at the church, a popular attraction for the tourists and others.
Fr Patricio Fernande, rector of the Basilica, who guided the president during his visit, said Kovind told him he feels blessed by coming to the medieval-era heritage monument and had visited the place earlier as well.
"He was also happy that this time when he visited Goa, there are rains in the state. So he said besides the blessings from the church, God is also blessing (Goa) in the form of rains," the priest said.
"I briefed him on the significance of the church and its history. I also told him about the incorrupt body of St Francis Xavier (preserved in the church) which is nothing sort of a a miracle," he said.
"So I prayed for him and also for the country. Then I took him inside and showed him the golden rose where he clicked pictures with us. The rose had been given to the Diocese of Goa by the Pope (as a token of reverence0," he said.
At the Mangueshi Temple, Kovind took blessings of Lord Manguesh (considered an incarnation of Lord Shiva) before heading back to Panaji.
The shrine is perhaps the most famous of all Goan temples and attracts a large number of tourists.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)