Complexation during the sorption of palladium(II) ions from chloride media by chemically modified silicas has been studied. Due to the use of mesoporous silicas with an average pore diameter of >10 nm for their synthesis, these sorbents do not change their volume in aqueous and organic media and have high mass transfer characteristics. The dependences of the sorption of Pd(II) ions from chloride solutions under static conditions as a function of time, HCl concentration, and Cl– ion have been obtained; sorption isotherms are constructed. Based on the experimental data, a conclusion has been made about the coordination mechanism of sorption, which has been proved by a combination of spectral methods (IR, UV-VIS, and X-ray photoelectron spectroscopy). The structure of sulfur-containing sorbents and their complexes with palladium has been modeled using the DFT M06 quantum-chemical method in the def2tzvp basis in the gas phase and taking into account the H2O solvent. The performed calculations make it possible to substantiate the nature of the dependence of sorption on the acid concentration and to confirm the formation of palladium(II) complexes with bidentate coordination of ligands in the silica phase modified with thiosalicylic and mercaptoacetic acids.