The Pope appealed to Catholics and Lutherans to "mend" history and look with honesty at the past, "recognising error and seeking forgiveness".
By tradition, on 31 October 1517 the German theologian Martin Luther nailed his 95 theses to the door of a church.
The papal visit kicks off a year of events to mark the quincentenary.
Pope Francis and Lutheran leaders presided over a ecumenical prayer service in Lund cathedral in southern Sweden on Monday.
