In minimal processing industry, chlorine is widely used in the disinfection process and ultrasound (US) increases the disinfection efficacy of chlorine and reduces the cross-contamination incidence during washing. Tap water (TW), which has no disinfection effect, is generally used to rinse off sanitizer residues on the surface of disinfected fresh-cut vegetables. In this study, aqueous ozone (AO), a low-cost and residue-free sanitizer, was used to replace TW rinsing in combination with US (28 kHz)–chlorine (free chlorine [FC] at 10 ppm, a concentration recommended for industrial use) for the disinfection of fresh-cut lettuce as a model. US–chlorine (40 s) + 2.0 ppm AO (60 s) treatment resulted in browning spots on lettuce surface at the end of storage. In contrast, US–chlorine (40 s) + 1.0 ppm AO (60 s) did not lead to deterioration of the sensory quality (sensory crispness, color, and flavor) and a change in total color difference, and the activities of browning-related enzymes were significantly lower. Moreover, US–chlorine (40 s) + 1.0 ppm of AO (60 s) treatment led to significantly lower counts of Escherichia coli O157:H7, Salmonella Typhimurium, aerobic mesophilic (AMC), and molds and yeasts (M&Y) on days 0–7 than US–chlorine (60 s) + TW (60 s) and single 1.0 ppm AO (120 s) treatments, suggesting that AO provided an additional disinfection effect over TW, while reducing the overall processing time by 20 s. Cell membrane permeability analysis (alkaline phosphatase, protein, nucleotide, and adenosine triphosphate leakage) showed that the combination with 1.0 ppm AO caused more severe cell membrane damage in E. coli O157:H7 and S. Typhimurium, explaining the higher disinfection efficacy. 16S rRNA sequencing revealed that following US–chlorine (40 s) + 1.0 ppm of AO (60 s) treatment, Massilia and Acinetobacter had higher relative abundances (RAs) on day 7 than after US–chlorine (60 s) + TW (60 s) treatment, whereas the RAs of Escherichia–Shigella was significantly lower, indicating that the former treatment has a superior capacity in maintaining a stable microbial composition. This explains from an ecological point of view why US–chlorine (40 s) + 1.0 ppm of AO (60 s) led to the lowest AMC and M&Y counts during storage. The study results provide evidence that AO has potential as an alternative to TW rinsing to increase the disinfection efficacy of US–chlorine.