The existing body of literature has witnessed extensive research efforts dedicated to exploring the impact of supplementary cementitious materials (SCMs) possessing pozzolanic characteristics on concrete. Nevertheless, the holistic concept of micro-scale fillers has frequently been a subject that remains insufficiently explored. This study endeavors to formulate binary cementitious systems that incorporate silica fume (SF) and micro-quartz filler (MQF) to enhance the durability and mechanical properties of cementitious concrete. We systematically investigate the effects of varying replacement levels of SF and MQF, alongside changes in the water-to-binder (w/b) ratio. With w/b ratios spanning 0.25 to 0.40, we explored replacement levels of 8, 10, and 12% (wt.) for SF, and 5, 8, 10, 15, 25, and 35% (wt.) for MQF. The findings revealed a consistent decrease in porosity and permeability as the replacement levels increase. Notably, a marked increase in compressive strength is observed with SF replacement, reaching its peak at an 8% MQF replacement level. Even as MQF replaces 15% of SF, concrete mixtures with 12% SF consistently exhibit superior strength. Importantly, MQF’s ultrafine particle size mirrors SF’s impact on enhancing compressive strength, porosity reduction, and permeability, despite its high crystalline structure. The study employs an analysis of variance (ANOVA) to rigorously assess the influence of each variable on the studied responses.