The increasing ozone concentration in Asia impedes rice production. Applying plant growth-promoting bacteria (PGPB) is one of the biological tools to improve agricultural production. However, underlying mechanisms are still unclear. In this study, PGPB, including Bacillus thuringensis (BT), Lysinibacillus sp. N5 (N5) and Bacillus sp. N7 (N7), were added as inoculants to Oryza sativa L. ssp. indica cv. Pathumthani 1 (PTT1) and Oryza sativa L. ssp. indica cv. RD41 (RD41). Rice productivity without bacterial inoculation in PTT1 was higher than that of RD41 under ambient air. Moreover, inoculation with BT and N7 was more effective in improving appearances of rice (seed length and seed width) for both cultivars under ambient air. Elevated ozone levels can significantly decrease indole-3-acetic acid (IAA), photosynthesis rate and ascorbic acid content, resulting in decreased rice yields. Inoculating PGPB (BT, N5 and N7) significantly increased rice quality as 100-grain weight and seed width under ozone stress. Rice inoculated with N5 and N7 performed best under high ozone levels; these bacteria could alleviate ozone stress by increasing IAA production, photosynthesis capability and ascorbic acid content. In addition, rice inoculated with bacteria had lower malondialdehyde (MDA) than rice without inoculation under ozone stress. Therefore, the application of a suitable microorganism as a biofertiliser could be an alternative biological tool to mitigate rice yield losses under ozone stress.