Pilgrims from around the world packed St Peter's Square in soaring temperatures as the Pope carried out the canonisation.
Local authorities handed out a million bottles of water and the fire brigade was at the ready to spray the crowds with water to relieve them from the heat.
Padre Pio, an Italian Capuchin monk who died in 1968, is revered for having borne permanent wounds on his hands and feet like those Christ suffered at the crucifixion.
Church doubters
"We inscribe in the roll of saints, and we declare in the entire Church that he is honoured with devotion among the saints," the Pope said in Latin.
Pope John Paul II is said to have a special affection for Padre Pio, and as a young man travelled to his monastery in southern Italy for confession.
The approval of Padre Pio's sainthood has taken place in record time, but during his lifetime many in the Church doubted claims of his miracles and suggested he was a fraud.
He was said to have known what penitents would confess to him and reportedly wrestled with the devil in his cell.
Doctors never found a medical explanation for his bleeding hands and feet which never healed but never became infected.
In granting him sainthood, the Church officially recognised two of his miracles - the curing of an 11-year-old boy who was in a coma and the medically inexplicable recovery of a woman with lung disease.
Even before his canonisation, Padre Pio's former monastery at San Giovanni Rotondo had become a major site of pilgrimage for Catholics from around the world.