With growing public awareness of metabolic health, there is increasing demand for bakery products with a low glycemic index (GI) and enhanced functional properties. This study developed brownies with improved nutritional profiles by partially replacing sugar and cocoa powder with carob syrup and carob flour at different levels. Five formulations (F1–F5) were prepared as follows: the control (T) contained 26% sugar and 5% cocoa powder without carob syrup or flour; F1 contained 20% sugar, 6% carob syrup, and 5% cocoa powder; F2 had 16% sugar, 10% carob syrup, and 5% cocoa powder; F3 included 13% sugar, 13% carob syrup, 3% cocoa powder, and 2% carob flour; F4 contained 16% sugar, 10% carob syrup, 4% cocoa powder, and 1% carob flour; and F5 contained 13% sugar, 13% carob syrup, 4% cocoa powder, and 1% carob flour. All formulations were evaluated for physicochemical properties, antioxidant capacity, texture, oxidative stability, and sensory acceptability. Formulations containing 13% carob syrup combined with 1–2% carob flour (F3 and F5) showed significantly higher antioxidant capacity than others. F5 exhibited the best oxidative stability, with an increased induction time, and received the highest sensory scores for taste, texture, and intent to purchase, which was over 84%. Its GI was estimated at 48, which is substantially lower than the control brownie (GI = 100), indicating a significantly reduced glycemic response. Moreover, in vitro gastrointestinal digestion using the standardized INFOGEST protocol demonstrated retention of over 77% of total polyphenols after digestion, indicating high bioaccessibility of antioxidant compounds. These findings highlight carob syrup and flour as sustainable, effective, and natural ingredients to enhance the nutritional and functional quality of baked goods without compromising consumer appeal. This study strongly supports the development of functional, low-GI bakery products that meet the evolving needs of health-conscious consumers worldwide.