Ferroviaria's Patricia Sochor broke the deadlock after seven minutes when her long-range free-kick evaded everyone before slipping through the hands of America’s goalkeeper.
America drew level through a Catalina Usme penalty, but Ferroviaria regained their lead just three minutes later with a penalty of their own, dispatched by Aline Milene.
The Brazilian club managed to hold the 2-1 scoreline to the end, with their win making boss Lindsay Camila the first female coach to win the competition.
Ferroviaria have won the tournament once before, in 2015.
The next edition of the Copa Libertadores Femenina will be hosted by Chile in September/October this year.