The 79-year-old pontiff tripped on a steps at the altar and had to be helped to his feet by the Vatican's master of ceremonies, Guido Marini.
Francis was apparently uninjured and amid tight security finished the event, which was aired to a television audience of millions.
The hill-top shrine is home to an ancient Catholic icon believed to work miracles.
During the open-air mass attended by tens of thousands of people, Francis thanked citizens of the former Communist-ruled nation for keeping their faith through adverse times.
Francis held mass at Jasna Gora before he headed to the World Youth Day celebrations in the southern Polish city of Krakow, being attended by some 1.5 million young people from around the world.
The five-day visit is the first by Francis to Poland, one of Europe's most deeply Catholic nations.
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