Abscisic acid (ABA) plays a key role in promoting the growth and development of plants, as well as mediating the responses of plants to adverse environmental conditions. Here, we measured the photosynthetic capacity of wild-type RR, mutant sitiens (sit), and ABA-pretreated sit tomato seedlings following exposure to low-temperature (LT) stress. We found that the net photosynthetic rate, intercellular carbon dioxide concentration, transpiration rate, and stomatal conductance of sit seedlings were lower than those of RR seedlings under LT stress. The chloroplast width, area, and number of osmiophilic granules were significantly larger in sit seedlings than in RR seedlings, while the chloroplast length/width ratio was significantly lower in sit seedlings than in RR seedlings. The photochemical activity of sit seedlings was lower, and the expression of photosynthesis-related genes in sit seedlings was altered following exposure to LT stress. ABA pretreatment significantly alleviated the above phenomenon. We also conducted an RNA sequencing analysis and characterized the expression patterns of genes in tomato seedlings following exposure to LT stress. We constructed 15 cDNA libraries and identified several differentially expressed genes involved in photosynthesis, plant hormone signaling transduction, and primary and secondary metabolism. Additional analyses of genes encoding transcription factors and proteins involved in photosynthesis-related processes showed pronounced changes in expression under LT stress. Luciferase reporter assay and electrophoretic mobility shift assay revealed that WRKY22 regulates the expression of PsbA. The PSII of WRKY22 and PsbA-silenced plants was inhibited. Our findings indicate that ABA plays a role in regulating the process of photosynthesis and protecting PSII in tomato under LT stress through the WRKY22–PsbA complex.