In this work, the inactivation of the waterborne antibiotic-resistance bacteria (ARB) Klebsiella pneumoniae (K. pneumoniae) has been evaluated to reduce the health risk in hospital environments by using an absorption process employing an ozone gas stream generated by commercially available electro-ozonizers (MIKROZON® cell). The ozone mass flow generated in the gas stream ranges from 0.026 to 0.047 mg min−1 depending on the applied intensity (0.1, 0.25, or 0.5 A). The results show that the disinfection rate improves as the mass flow of ozone gas increases and is significantly influenced by the organic matter content of the target liquid solutions. Specifically, log reductions of 1, 4, and 6 were achieved at the end of the 180-min treatment of hospital urine when intensities of 0.1, 0.25, and 0.5 A were applied, respectively. In addition, the logarithmic removal of four Antibiotic Resistance Genes (ARGs) was investigated to control the spread of antibiotic resistance through horizontal transfer processes. Logarithmic removals of 5.43, 3.17, 3.04, and 2.89 were obtained for aac(6′)-Ib, blaTEM, blaSHV, and blaKPC, respectively, during the treatment of urine (0.047 mg min−1 of ozone gas). A comprehensive comparison of the removal of these four ARGs with other disinfection technologies is also provided. It can be concluded that this work presents promising results that have the potential to increase the technology readiness level of the MIKROZON® ozone generator, as it demonstrates the ability to enhance the disinfection process of highly organic liquid effluents.