The pontiff gave a video message to the tens of thousands of people at the stadium in Houston, Texas, before the game.
He said the event was "a sign of peace, friendship and solidarity for the world" just minutes before Gaga, dressed in a metallic leotard emblazoned with sequins and wearing knee length boots, dived into the stadium.
On this special day, we bring you a very special message from Pope Francis (@Pontifex). #SB51 pic.twitter.com/LtNlcpCnYy
— Houston Super Bowl (@HouSuperBowl) February 5, 2017
She performed Poker Face, Born This Way and Telephone before donning a gold jacket with spiked shoulders for her rendition of Just Dance.
Celebrities in the crowd included Sir Elton John, John Travolta, Mark Wahlberg, Usher, John Legend and his wife Chrissy Teigen and Brady's wife, model Gisele Bundchen.
In his pre-recorded Spanish message Francis made history by becoming the first pontiff to address a Super Bowl.
"Great sporting events like today's Super Bowl are highly symbolic," he said, "showing that it is possible to build a culture of encounter and a world of peace".
"By participating in sport, we are able to go beyond our own self-interest and in a healthy way we learn to sacrifice, to grow in fidelity and respect the rules."
The New England Patriots were once again crowned Super Bowl champions having fought back from 25 points behind to defeat the Atlanta Falcons 34-28 in overtime.
