Tomato plants were grown with a drip irrigation system to evaluate the effects of a novel organo-mineral fertilizer [2:10:1 (w/w/w) mixture of calcium sulphate, ground rice bran, and humic acid] (OMF), which can mitigate salinity stress, on plant growth, fruit yield, and the incidence of blossom-end rot (BER) under salinity stress. Salinity stress was applied by drip irrigation with 50 mM of NaCl. Plant growth with OMF was lower than that with chemical fertilizer (CF). Higher levels of K and P were obtained in the leaves from plants grown with OMF. OMF inhibited Na accumulation and proline increase in the leaves and was considered to alleviate salinity stress. Salinity treatment caused a decrease in fruit weight and an increase in ascorbic acid, sucrose, glucose, fructose, and glutamic acid. Tomato plants grown with OMF had smaller fruit than with CF without salinity, but the incidence of BER under salinity was reduced by OMF. The water soluble Ca content of the distal half of young tomato fruit was significantly decreased with salinity treatment. The incidence of BER under salinity was significantly lower in OMF than in CF, but there was no difference in the concentration of every form of Ca between CF-salinity and OMF-salinity treatments. The reduction in BER incidence with OMF treatment could not be explained by the differences in Ca concentration. The mechanism of the reduction in BER with OMF was not clear, so further studies are necessary.