Yoghurt has been known as an excellent source for delivering viable lactic acid bacteria (LAB) in concentrations providing benefits to the human host and microbiome. Different gastrointestinal tract (GIT) simulators have been developed and are successfully used to determine the viability of LAB from fermented dairy products in vitro studies. Commercial yoghurts were tested for digestibility using the GIT IT system Labfors 5 (INFORS HT, Switzerland). The length for both the gastric phase and the small intestinal phase was 120 min each. Yoghurt LAB colony-forming units were analysed prior to the GIT simulation test, as well as after the simulation test. The survival rate of LAB was evaluated based on the differences in the viable LAB count at the beginning and at the end of the experiment. Tested yoghurts’ LAB were tolerated in the simulated gastric and small intestinal phases. Samples collected prior to and after the intestinal phase revealed that LAB had adapted and started to grow within 120 min. Our results showed the ability of LAB to recover in the intestinal phase which has been explained by the food matrix, which protects the bacteria from the elimination effect of intestinal secretions. In addition, differences in survival rates of LAB significantly influenced the overall LAB colony-forming units in the gastrointestial tract. The chemical composition of the product has an influence on the survival rate of LAB, and it should be studied more thoroughly. In vitro studies are quite different from the assay in vivo studies; however, this information provides significant data about the viability of LAB from regularly consumed products and helps to modulate the influence of LAB on human microbiota.