Separating functionalized single-wall carbon nanotubes (SWCNTs) from functionalized amorphous carbon is challenging, due to their polydispersity and similar physicochemical properties. We describe a single-step, dialytic separation method that takes advantage of the ability of heavily functionalized SWCNTs to bundle in a polar environment while maintaining their solubility. Experiments on functionalized SWCNTs were compared with functionalized, C60 fullerenes (buckyballs) to probe the general applicability of the method and further characterize the bundling process. This approach may simultaneously be used to purify a functionalization reaction mixture of unreacted small molecules and of residual solvents, such as dimethylformamide.