Drought-tolerant plant growth-promoting rhizobacteria (PGPR) may promote plant development under limited water supply conditions, when plant’s water demand is not completely satisfied under rain-fed conditions or when irrigation water availability is limited. The aim of this study was to examine the effects of two inoculation treatments (B2: Alcaligenes sp. 3573, Bacillus sp. BAR16, and Bacillus sp. PAR11 strains and B3: Pseudomonas sp. MUS04, Rhodococcus sp. BAR03, and Variovorax sp. BAR04 strains) and compare those to a control (B0) without artificial inoculation on chlorophyll fluorescence, leaf chlorophyll content (SPAD value), canopy temperature, and the yield of the processing tomato cultivar H-1015 F1 grown under field conditions. The young seedlings of the hybrid tomato variety H-1015 F1 were immersed in 1% of B2 or B3 products (BAY-BIO, Szeged Hungary) for 5 min. Inoculated and untreated seedlings were grown under three irrigation treatments [regular irrigation (RI), deficit irrigation (DI), and no irrigation (I0)], to reveal the effect of PGPR under different levels of water stress. In the dry year (2018), higher canopy temperature and chlorophyll fluorescence (Fv/Fm) were measured during flowering in plants treated with bacteria than in untreated plants. In the stage of flowering and fruit setting, the B3 treatment led to a significant decrease in the Fv/Fm value, canopy temperature remained high, and the SPAD value was statistically the same in all treatments. Under limited water supply, in most cases, PGPR led to a significantly greater total yield but more unripe green berries compared to untreated plants. Under moderate water shortage (dry year + deficit irrigation), the B3 treatment resulted in 26% more ripe, marketable fruit and 49% less unripe fruit compared to the B2 treatment. On the other hand, in the wet year (2020), the bacterial treatments generally did not affect physiological properties, though the B2 treatment produced a higher marketable yield while the amount of green and diseased fruits did not differ statistically, compared to the B3 treatment under deficit irrigation. Based on our study, we recommend the application of the B3 PGPR product as it positively affected key physiological processes, leading to a higher marketable yield particularly under water shortage.