"Notiomastodon" belongs to the family Gomphotheriidae, a group of animals distantly related to modern elephants and mammoths. "Notiomastodon" seems to have had a 4-million-year-long ghost lineage, diverging from the clade that contains "Rhynchotherium" and "Cuvieronius" around the Late Miocene. This would imply that "Notiomastodon" had been evolving in southern Central America, where the fossils are poorly sampled, prior to its migration into South America during the Pliocene or Pleistocene. Gomphotheres arrived in South America after the formation of the Isthmus of Panama as part of the Great American Biotic Interchange, alongside many other taxa from North America. The oldest known record of gomphotheres in South America is a fragmentary vertebra from the Earliest Pleistocene (about 2.5 Mya) Uquia Formation of Argentina. The oldest known remains definitively attributable to "Notiomastodon" are known from the late Early Pleistocene (1.2-0.8 Mya) from the Rio de la Plata, also in Argentina, consisting of a pair of tusks and other associated remains. A 2019 study using collagen sequencing found "Notiomastodon" closer to "Mammut" than to extant elephants, though how this affects gomphothere phylogeny is unclear.