Legionnaires’ disease remains a serious health problem globally, caused by the Gram-negative bacteria Legionella. The study objective was to characterize the ability of ozone to kill viable but non-culturable (VBNC) Legionella and examine the kinetic characteristics of VBNC Legionella inactivation. The removal of the living Legionella by ozone was highest (>99%) among VBNC, living (culturable, no including VBNC), and dead Legionella trials. Ozone can kill VBNC Legionella at a more rapid rate than the other Legionella states. Ozone can fragment Legionella into small DNA fragments and can damage the Legionella cell membranes and DNA. Based on our results, the killing process was characterized as follows. Ozone oxidizes living Legionella to VBNC Legionella and then oxidizes VBNC Legionella to dead Legionella. Ozone damages the dead Legionella cell membrane and enters the dead Legionella body. Ozone decomposes dead Legionella DNA into small DNA fragments. The VBNC Legionella inactivation kinetic process in the wastewater was expressed mathematically. These equations can be used widely for predicting variations of VBNC Legionella concentrations and thus as a framework for controlling the activity of the bacteria and, ultimately, Legionnaires’ disease.