High-methoxyl pectin (HMP, 72.5 % esterification degree and galacturonic acid content of 67.9 %) was extracted from grape pomace using a sequential ultrasound-microwave extraction. The extracted HMP was used to develop low-fat synbiotic set yogurts containing probiotic cells. Higher grape pomace pectin (GPP) concentrations (0.5-2 %) increased the probiotic bacterial population of Lactobacillus acidophilus LA-5 and Bifidobacterium bifidum BB-12. Higher cell viability was observed for L. acidophilus LA-5 compared to B. bifidum BB-12. A response surface optimization showed that the presence of 8.08 Log CFU mL-1L. acidophilus LA-5 and 1.88 % HMP experimentally resulted in the best probiotic viability (10.83 ± 0.11 Log CFU mL-1), overall acceptability (8.03 ± 0.06), and pH (4.25 ± 0.05) values. Compared to pectin-free probiotic yogurts, the optimal yogurt gels presented higher probiotic survivability, lower syneresis, and superior storage-dependent sensory attributes during 21 days of storage. However, a 14-day storage period was generally deemed suitable. The GPP-containing yogurt compared to the pectin-free sample exhibited higher colloidal stability with a larger particle size (433.8 nm vs. 272.5 nm) and lower zeta potential (-20.4 mV vs. -10.6 mV). Field emission-scanning electron (FE-SEM) and fluorescent (FLM) microscopy images confirmed a denser microstructure for GPP-enriched yogurts. The chemical interactions in the yogurt were not affected by enriching with GPP as investigated by FTIR, whereas the steady and dynamic rheological properties were significantly improved. GPP-enriched yogurt had a firmer gel structure with a larger linear region and lower G' compared to the control, indicating a semi-solid state. The GPP as a multi-functional prebiotic ingredient would be promising in designing healthier food products.