We consider a nanoelectromechanical Josephson junction, where a suspended nanowire serves as a superconducting weak link, and show that an applied dc bias voltage can result in suppression of the flexural vibrations of the wire. This cooling effect is achieved through the transfer of vibronic energy quanta first to voltage-driven Andreev states and then to extended quasiparticle electronic states. Our analysis, which is performed for a nanowire in the form of a metallic carbon nanotube and in the framework of the density matrix formalism, shows that such self-cooling is possible down to the ground state of the flexural vibration mode of the nanowire.