Greek yogurt is a fermented dairy product of high nutritional value that can be used as a matrix for the delivery of probiotics. The aim of this study was to develop a new probiotic Greek sheep yogurt with upgraded quality and functional characteristics. To do this, yogurt was manufactured by fermenting pasteurized milk with the commercial starter culture (Streptococcus thermophilus (ST), Lactobacillus bulgaricus (LB)) together with a probiotic Lacticaseibacillus rhamnosus (LR) wild-type strain (probiotic yogurt; PY). As a control, yogurt manufactured with only the starter culture (ST, LB) was used (conventional yogurt; CY) The survival of all three lactic acid bacteria (LAB) species (ST, LB, and LR) was monitored throughout the products’ shelf life (storage at 4 °C for 25 days), and also following exposure to a static in vitro digestion model (SIVDM). The population dynamics of total aerobic plate count (APC), Enterobacteriaceae, yeasts and molds grown in both yogurts were also determined. The total antioxidant activity (AA) of yogurts was comparatively determined using in parallel two different assays, whereas the Folin-Ciocalteu assay was used to determine their total phenolic content (TPC). At each sampling day, yogurts were also evaluated for their pH, titratable acidity (TA) and main sensory characteristics. The population of probiotic LR remained stable during the shelf life (and above 108 CFU/g). Yogurt starters (ST, LB) were not detected following SIVDM, whereas LR (in PY) presented a reduction of about only one log. The AA and TPC of PY were found significantly higher than that of CY (P < 0.05). At the end of storage (25th day), neither pH nor TA differed significantly between the two yogurt types, while no fungal growth was observed in the PY. Consumer sensory analysis did not reveal important differences between the two yogurt types during their shelf life. To sum up, the novel yogurt was able to deliver to consumers a high number of probiotic cells (>108 CFU/g), presented increased antioxidant power, had an expanded shelf life, and maintained its good sensory attributes.