We investigate the scattering off dilute magnetic impurities placed on the surface of three-dimensional topological insulators. In the low-temperature limit, the impurity moments are Kondo-screened by the surface-state electrons, despite their exotic locking of spin and momentum. We determine signatures of the Kondo effect appearing in quasiparticle interference (QPI) patterns as recorded by scanning tunneling spectroscopy, taking into account the full energy dependence of the T matrix as well as the hexagonal warping of the surface Dirac cones. We identify a universal energy dependence of the QPI signal at low scanning energies as the fingerprint of Kondo physics, markedly different from the signal due to nonmagnetic or static magnetic impurities. Finally, we discuss our results in the context of recent experimental data.