The issues of lactose intolerance and vegetarianism have encouraged the introduction of non-dairy fermented food into the market. Therefore, this study aims to evaluate the effect of agitation speed on the bioactive compounds and functional characteristics of probioticated pomegranate juice. Pomegranate juice was fermented with Lactobacillus casei at different agitation speeds ranging from 0 (microaerophilic) to 150 rpm at 37 °C. The functional properties of probioticated pomegranate juice were evaluated in terms of growth (biomass), lactic acid production, antioxidant activity, total phenolic content, and key metabolites using LC-MS/MS. The growth kinetics of fermentation was monitored at the optimal condition using one factor at a time method. High cell growth (3.58 × 1010 cfu/mL or 7.9 gL−1) was observed for L. casei probioticated pomegranate juice agitated at 0 rpm. The findings of this study reveal the potential of pomegranate juice as a medium for L. casei cultivation without nutrient supplementation. The improvement of antioxidant activity in the probioticated juice could be due to the increment of quercetin-3-glucoside. Therefore, L. casei grew well in pomegranate juice with a high cell viability and antioxidant activity at a non-agitated condition. Probioticated pomegranate juice is a potentially functional drink.