Small black soybeans (Seomoktae, SBS), traditionally regarded as medicinal beans in East Asia, contain abundant bioactive compounds with antioxidant and anti-inflammatory potential. This study aimed to develop a functional plant-based milk substitute by fermenting soymilk (yellow soybean, YS) supplemented with SBS (25% or 50%) using Streptococcus thermophilus JAMI_LB_02 and Lactiplantibacillus plantarum JAMI_LB_05 (patented LABs) to enhance probiotic functionality and nutritional value. Fermentation characteristics, microbial viability, antioxidant activity, anthocyanin content, and free amino acid profiles were evaluated. After 72 h, total acidity in all samples exceeded 0.81%, and viable LAB counts reached 10.07–10.21 log CFU/mL, surpassing the Korean Food Code. The 50% SBS formulation exhibited significantly higher radical scavenging activity, total phenol and flavonoid contents, and anthocyanin levels (p < 0.05). Digestive enzyme treatment increased total free amino acid in SBS 50%, particularly functional amino acids such as arginine, alanine, and asparagine. Heatmap analysis classified products with high SBS content as Group A and analyzed the correlation between redness, antioxidant activity, and water-soluble amino acid content. Overall, SBS-fermented soymilk is an improved protein digestibility, probiotic-rich, and alternative to dairy-based fermented products, aligning with the growing consumer demand for plant-based functional foods.