Vast amounts of information can be obtained by systematic explorations of synergy between phytochemicals and probiotics, which is required for the development of non-dairy probiotic products, globally. Evidence confirms that the same probiotic strain can have different efficiencies depending on the food matrix. One such functional property, viz., antipathogenicity of the probiotic strain against Shigella was investigated in this study. The potential of two fruit based (apple and sea buckthorn) beverage matrices fortified with Lactobacillus rhamnosus GG (ATCC 53103), against outbreak-causing serotypes of Shigella dysenteriae (ATCC 29026) and Shigella flexneri (ATCC 12022) was evaluated. The originality of this study lies in the fact that the functionality assessment was performed with a more realistic approach under storage conditions from 0–14 days at 4 °C. The finding confirms that Lactobacillus rhamnosus GG (LGG) differs in its potential depending on beverage matrices. Principal Component Analysis (PCA) clustered the matrices based on their pathogen clearance. LGG fortified sea buckthorn beverage matrix showed 99% clearance of S. dysenteriae within the first hour compared to 11% in apple beverage matrix. Interestingly, S. flexneri showed more resistance and was cleared (99%) in the LGG fortified sea buckthorn beverage matrix within three hours compared to 5.6% in apple matrix.