The low-temperature (12 K) adsorption of single Au atoms on Si(100) is studied by scanning tunneling microscopy (STM). Comparison between experimental and calculated STM topographies as well as density-functional-theory calculations of the adsorption energies enable us to identify two adsorption configurations of Au atoms between Si-dimer rows (BDRs) and on top of Si-dimer rows (TDRs). In both adsorption configurations, the Au atoms are covalently bound to two Si atoms through a partial electron transfer from Si to Au. STM manipulation confirms that the TDR adsorption configuration is metastable, whereas the BDR one is the most stable configuration.