The pop superstar performed at the Wells Fargo Center just days before the Pontiff is due to head to the city as part of his U.S. visit.
Madonna made reference to his trip while on stage, joking that he is visiting the same cities as her Rebel Heart Tour.
She told the audience, 'The pope is stalking me. Either he's a copycat or he's secretly in love with me.'
The Like A Virgin hitmaker, who was raised a Catholic, also talked about her issues with the Church. She has previously infuriated Catholic leaders with religious themes in her videos and stage show.
Madonna even incurred the wrath of the Catholic League by including dancers dressed as nuns on her current tour.
'Rules are for fools. That's why I like the new pope. He seems very open-minded,' she declared at the gig. 'I've been excommunicated from the Catholic Church three times. It shows the Vatican really cares.'
She went on to dedicate her version of La Vie en Rose to the Pope, saying, 'Since Popey-wopey is on his way over here (to Philadelphia), I want to dedicate this song to him.'