The use of topological edge states for spintronic applications could be severely hampered by limited lifetimes due to intrinsic many-body interactions, in particular electron-phonon coupling. Previous works to determine the intrinsic coupling strength did not provide a coherent answer. Here, the electron-phonon interaction in the metallic surface state of 3D topological insulators is revised within a first principles framework. For the archetypical cases of Bi2Se3 and Bi2Te3, we find an overall weak coupling constant of less than 0.15, but with a characteristic energy dependence. Derived electronic self-energies compare favorably with previous angle-resolved photoemission spectroscopy results. The prevailing coupling is carried by optical modes of polar character, which is weakly screened by the metallic surface state and can be reduced by doping into bulk bands. We do not find any indication of a strong coupling to the A1g mode or the presence of a Kohn anomaly in the surface phonon spectrum. The weak intrinsic electron-phonon coupling guarantees long-lived quasiparticles at elevated temperatures.