We report the mechanically induced formation of a silicon–hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a noncontact atomic force microscope (NC-AFM), a single hydrogen atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen-passivated surface and can be transferred to the tip apex, as evidenced from a unique signature in frequency shift curves. In the absence of tunnel electrons and electric field in the scanning probe microscope junction at 0 V, the hydrogen atom at the tip apex is brought very close to a silicon dangling bond, inducing the mechanical formation of a silicon–hydrogen covalent bond and the passivation of the dangling bond. The functionalized tip was used to characterize silicon dangling bonds on the hydrogen–silicon surface, which was shown to enhance the scanning tunneling microscope contrast, and allowed NC-AFM imaging with atomic and chemical bond contrasts. Through examples, we show the importance of this atomic-scale mechanical manipulation technique in the engineering of the emerging technology of on-surface dangling bond based nanoelectronic devices.