This study investigated the development and characterization of novel probiotic edible films based on kefiran (K), pullulan (P), and their blend (K/P) incorporated with Bacillus coagulans GBI-30, 6086 (BC30) or Saccharomyces (S.) boulardii. The influence of polymer composition and probiotic type on the physicochemical, barrier, structural, thermal, and biological properties was evaluated. All films were transparent, homogeneous, and flexible. Blending kefiran with pullulan effectively reduced the water sensitivity of pullulan while maintaining high brightness. FTIR analysis revealed spectral shifts in the O–H stretching region, suggesting intermolecular hydrogen-bonding interactions between kefiran and pullulan. DSC and AFM analyses demonstrated that S. boulardii increased nanoscale surface roughness and altered surface morphology, whereas BC30 spores functioned as dispersed filler particles, enhancing thermal stability with a Tpeak of 90.33 °C. BC30 exhibited the highest survival during simulated gastrointestinal digestion in pullulan-based films, whereas S. boulardii showed higher gastric sensitivity but maintained the highest post-digestion viability in P + S films (8.63 log CFU/g). Antimicrobial assays revealed that BC30-incorporated films showed selective inhibition, with K + B and K/P + B formulations producing inhibition zones of 27.50 ± 0.70 mm against Listeria monocytogenes ATCC 7644 and 25.50 ± 0.70 mm against Escherichia coli ATCC 25,922, respectively, while S. boulardii also demonstrated notable activity against Klebsiella pneumoniae. The high-water solubility and rapid biodegradability of pullulan-based films indicate their potential as eco-friendly active packaging materials. Overall, the K/P blend provided a structurally stable matrix and protective scaffold for probiotics, offering a promising functional packaging system with demonstrated biological activity.