The synthesis and characterization of stable gold nanoparticles (Au NPs) from gold chloride in soluble protein extracts of tomato (Solanum lycopersicum L.) leaves is demonstrated. This approach is a completely “green” synthetic method, which is simple, environmentally benign, and efficient, in contrast to conventional approaches that use toxic or hazardous chemicals, high temperature, pressure, and pH. As observed by transmission electron microscopy, the as synthesized nanoparticles were spherical and 13–15 nm in diameter. The agglomeration and electro-kinetic properties of the biologically reduced Au NPs were also studied. Au NPs with thiol and amino groups was successfully functionalized which was confirmed by investigation of Au NP self-assembly in the presence of L-cysteine.