The application of selenium (Se) to tomatoes enhances accumulation of bioactive compounds. The physiological window of Se is very narrow, and Se overdose reduces the yield. Glycine betaine was shown to reduce Se’s negative effects on plants and to potentiate its beneficial effects. In this study, baker’s yeast vinasse (BYV), as an affordable source of glycine betaine, was tested for its interaction with Se in an optimized foliar fertilizer. The application dose was selected after a laboratory experiment, wherein assays on plant height, leaves surfaces, stomatal conductance, and chlorophyll fluorescence were done. The Se and BYV supplemented foliar fertilizers were tested for their effects on accumulation of bioactives in drip-irrigated tomatoes cultivated in a greenhouse. Under laboratory conditions, assays demonstrated Se and BYV induced effects on tomatoes plants. Both the stomatal conductance and photosynthesis efficiency increased compared to a water treated control. The greenhouse experiment demonstrated that BYV and Se addition increases the number of tomato fruits in the “extra” marketable class and enhances the accumulation of ascorbic acid, carotenes, polyphenols, and flavonoids. The effects depend on the composition of the foliar fertilizer, the most significant effects being recorded for the foliar applied product with the highest BYV and nitrogen content.