The pontiff had already announced that he would be declaring the Spanish-born Serra a saint at a mass in Washington DC during his visit to the United States in September.
Opponents of the move had unsuccessfully petitioned the Vatican in a bid to block sainthood, as they had when Serra was beatified by John-Paul II in 1988.
John-Paul subsequently made a 1992 statement in which he formally asked for the forgiveness of native Americans for crimes committed during California's colonisation by European Christians.
Serra was accused of forcing many indigenous people to live in slave-like conditions in Catholic missions and of helping to destroy their languages and culture.