Thousands of Catholics attended the event at the Swedbank Arena.
On Monday, the Argentine pontiff made the historic step of expressing deep regret over the conflict between Catholics and Protestants on the 500th anniversary of the Protestant Reformation.
He appeared alongside heads of the Lutheran World Federation at an ecumenical service at Lund Cathedral, before attending a second ecumenical event at Malmö Arena in front of a large crowd.
At Tuesdays public mass he repeated his call for Swedens Catholics to set aside their differences with the countrys Lutheran majority.
Following the event, there was a farewell ceremony for him at Malmö airport before he departed for Rome.
There are thought to be around 150,000 Catholics in Sweden. Lutheranism is the main religion, but the country has a reputation for being strongly secular.