Blossom-end rot (BER) is a physiological disorder caused by calcium deficiency, often paired with moisture stress and irregular traditional watering practices. To understand the biological mechanism affecting the incidence of BER, different tomato genotypes were cultivated in sandy soil and were traditionally irrigated. Nine tomato genotypes were investigated to assess their susceptibility to BER, and the incidence rate varied from 7.1% in “Voskhod” to 57.6% in “Majnat” genotypes. This study also comprehensively analyzed various physiological and biochemical parameters to elucidate their correlation with BER incidence in tomato plants. Our findings revealed a range of parameters positively correlated with BER incidence, including the relative water content of roots, the number of fruits per plant, vitamin C content, and potassium content. Parameters related to fruit quality, such as titratable acidity, peroxidase content, and firmness degree, also showed positive correlations with BER incidence. Conversely, parameters such as total yield per hectare, chlorophyll content, average plant height, and calcium content demonstrated strong negative correlations with BER incidence, suggesting potential protective effects against this disorder. This study highlights that genotypes with higher marketable yields, such as ‘Voskhod’ (65 tons/ha), showed lower BER incidence, underscoring the importance of selecting the appropriate genotype in improving yield and reducing blossom-end rot in tomato fields. Conversely, cultivars with high BER sensitivity, such as ‘Chelnok’ (26.3 tons/ha), require specially designed cultivation management to avoid production declines.