The Argentine-born pope, the first pontiff from the Americas, has long been an advocate for indigenous groups and has highlighted their struggles.
During a 2015 visit to Bolivia, Francis apologized for the "grave sins" committed by Roman Catholic authorities against indigenous peoples during the colonial era.
The Mass on Wednesday featured various indigenous themes. At least one speaker spoke in the Mapuche language. People in Mapuche and other indigenous dress were prominent participants.
The Araucania region, like much of southern Chile, has seen vast tracts of trees felled for commercial development.
In his comments during the Mass, Francis deplored the "deforestation of hope," a reference to the marginalization of much of the indigenous community in the region.
People of indigenous background represent about 9 percent of the Chilean population, authorities say. The Mapuche are the nation's largest indigenous group, numbering some 1.4 million, mostly in the Araucania region.
Many of the Mapuches' grievances date from the 19th century, when the Chilean state, settlers and others took over much of the group's ancestral lands. The group lost additional land during the dictatorship headed by Gen. Augusto Pinochet beginning in 1973.
The return of democracy in 1990 has seen successive governments give land back to the Mapuches. But many indigenous activists call the land returns insufficient. Meantime, local land owners who are not Mapuche say they have been in the area for generations and are not responsible for past land thefts.
The Araucania is one of the poorest areas of Chile, which boasts one of Latin America's most dynamic economies. Many Mapuche communities live on small agricultural plots, farming potatoes and wheat, or make their living in the coastal fishing industry.
After the Mass, the pope was scheduled to meet with community leaders in a district that has seen violence related to what the Mapuches call a struggle for civil rights. Authorities say a minority of Mapuche activists has been violent.
In recent days, attackers have fire-bombed a number of churches in Santiago and near Temuco in apparent protests of the pope's visit. No one has been injured, and damage has been minor in the crude attacks, which typically feature gasoline placed in bottles and ignited. The strikes mirror similar attacks in recent years in the Araucania region.
Authorities have not publicly named any suspects in the series of church bombings.
(Los Angeles Times special correspondent Jorge Poblete in Santiago contributed to this report.)
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