Heterogeneous metal catalysts with bifunctional active sites are widely used in chemical industries. Although their improvement process is typically based on trial-and-error, it is hindered by the lack of model catalysts. Herein, we report an effective vacancy-pair capturing strategy to fabricate 12 heterogeneous binuclear-site catalysts (HBSCs) comprising combinations of transition metals on titania. During the synthesis of these HBSCs, proton-passivation treatment and step-by-step electrostatic anchorage enabled the suppression of single-atom formation and the successive capture of two target metal cations on the titanium-oxygen vacancy-pair site. Additionally, during acetylene hydrogenation at 20 °C, the HBSCs (e.g., Pt1Pd1-TiO2) consistently generated more than two times the ethylene produced by their single-atom counterparts (e.g., Pd1-TiO2). Furthermore, the Pt1Pd1 binuclear sites in Pt1Pd1-TiO2 were demonstrated to catalyze C2H2 hydrogenation via a bifunctional active-site mechanism: initially C2H2 chemisorb on the Pt1 site, then H2 dissociates and migrates from Pd1 to Pt1, and finally hydrogenation occurs at the Pt1-Pd1 interface.