Lack of appropriate seed extraction methods limits a sustainable supply of quality seed for tomato (Solanum lycopersicum L.). Natural fermentation and HCl acid methods are the most common methods used for tomato seed extraction. Short fermentation period causes inefficient mucilage removal while extended period causes spontaneous germination of seed during extraction. Lower concentrations of HCl acid cannot efficiently clean the gelatinous substance which inhibit germination though higher concentrations harm the embryo of seed affecting the seed physiology. This study was undertaken to determine effects of seed extraction method on physiological quality of tomato seed and developing seedlings. Fermentation (24, 48 or 72 h) and immersion in HCl acid at 1, 2, or 3% (V/V) for 30, 60 or 90 min were treatments. Tomato fruit pulp fermented for 24 h had a better seed germination percent which decreased after prolonged fermentation of 48 to 72 h. In contrast, the HCl acid seed extraction method produced bright seed with greater germination percent. The highest germination percent in Petri dish and pots was from immersion of tomato fruit pulp in 2% HCl acid for 60 min followed by immersion in the same concentration of HCl for 90 min. Germination percent was increased for every additional 30 min immersion in a 1% HCl concentration. At 2% HCl concentration, germination percent at 60 min was best compared with 30 and 90 min soaking. At 3% HCl, germination percent generally decreased with increasing immersion period. Seed extracted in 2% HCl for 60 min were superior in germination (99.33%), seedling emergence (89.76%), seedling length (14 cm), seedling fresh weight (558.1 g), seedling dry weight (26.73 g), and vigor-index I (1391) and II (2655). Seed were free from mycoflora. This seed extraction method can be used to produce high-quality seed, control seed-borne pathogens and produce vigorous tomato seedlings.