Sputtering of MoS2 films of single-layer thickness by low-energy argon ions selectively reduces the sulfur content of the material without significant depletion of molybdenum. X-ray photoelectron spectroscopy shows little modification of the Mo 3d states during this process, suggesting the absence of significant reorganization or damage to the overall structure of the MoS2 film. Accompanying ab initio molecular dynamics simulations find clusters of sulfur vacancies in the top plane of single-layer MoS2 to be structurally stable. Measurements of the photoluminescence at temperatures between 175 and 300 K show quenching of almost 80% for an ~10% decrease in sulfur content.