Invasive species can indirectly affect ecosystem processes via the disruption of mutualisms. The mutualism between the whistling thorn acacia (Acacia drepanolobium) and four species of symbiotic ants is an ecologically important one; ants strongly defend trees against elephants, which can otherwise have dramatic impacts on tree cover. In Laikipia, Kenya, the invasive big-headed ant (Pheidole megacephala) has established itself at numerous locations within the last 10–15 years. In invaded areas on five properties, we found that three species of symbiotic Crematogaster ants were virtually extirpated, whereas Tetraponera penzigi co-occurred with P. megacephala. T. penzigi appears to persist because of its nonaggressive behavior; in a whole-tree translocation experiment, Crematogaster defended host trees against P. megacephala, but were extirpated from trees within hours. In contrast, T. penzigi retreated into domatia and withstood invading ants for >30 days. In the field, the loss of defensive Crematogaster ants in invaded areas led to a five- to sevenfold increase in the number of trees catastrophically damaged by elephants compared to un-invaded areas. In savannas, tree cover drives many ecosystem processes and provides essential forage for many large mammal species; thus, the invasion of big-headed ants may strongly alter the dynamics and diversity of East Africa's whistling thorn savannas by disrupting this system's keystone acacia–ant mutualism.