It is quite challenging to avoid microdefect formation during hydrothermal growths and/or calcination processes, while manufacturing high-quality zeolite membranes in a reproducible manner. Even less than 1% of defects, which generally provide non-selective pathways, will considerably worsen the intrinsic, high molecular sieving-based separation performance of a continuous zeolite membrane. Herein, we propose a simple and reliable method for blocking defects using water-soluble dye molecules, which were originally used for the visualization of non-zeolitic, defective structures in a zeolite membrane. Since the dye molecules are ~1 nm in size, they cannot diffuse into the zeolitic pores and selectively access the defects. For the demonstration of dye-based defect healing, we chose a siliceous chabazite type SSZ-13 zeolite membrane (pore size = 0.37 × 0.42 nm2) with some degree of defects and investigated the effect of defect healing on the final CO2 separation performance. Since the defects were gradually filled by the dye molecules, both CO2/N2 and CO2/CH4 separation performances were concomitantly increased. Intriguingly, the CO2 perm-selectivity test with ternary mixtures including H2O vapor (the 3rd largest component in the flue and natural/shale/bio gas streams) in the feed diminished CO2 separation performance. This could be ascribed to inhibited transport of the fast permeating species, here CO2, from the adsorbed H2O molecules on the dye-treated and water-friendly (relatively hydrophilic) membrane surface. On the contrary, the intact, siliceous (water-repelling or hydrophobic) SSZ-13 membranes showed improved CO2 perm-selecitivities in the presence of H2O vapor, seemingly due to defect blocking by the physisorbed H2O molecules.