A rapid photothermal bacterial inactivation technique has been developed by irradiating near-infrared (NIR) light onto bacterial cells (Escherichia coli, Bacillus subtilis, Exiguobacterium sp. AT1B) deposited on surfaces coated with a dense, random array of nanoporous gold disks (NPGDs). With the use of cell viability tests and SEM imaging results, the complete inactivation of the pathogenic and heat-resistant bacterial model strains is confirmed within ~25 s of irradiation of the NPGD substrate. In addition to irradiation control experiments to prove the efficacy of the bacterial inactivation, thermographic imaging showed an immediate averaged temperature rise above 200 °C within the irradiation spot of the NPGD substrate. The light-gated photothermal effects on the NPGD substrate offers potential applications for antimicrobial and nanotherapeutic devices due to strong light absorption in the tissue optical window, i.e., the NIR wavelengths, and robust morphological structure that can withstand high instantaneous thermal shocks.