Owing to its excellent elasticity, wide spectral range of transparency, and outstanding chemical and thermal stability, polydimethylsiloxane (PDMS) is an elastomer of great technological importance, being widely used in the fabrication of microfluidic and optofluidic devices in particular. Compact, low loss optical waveguides are crucial in such devices for a dense integration of optical functionalities. Compared with photolithographic methods, multiphoton laser direct writing through photopolymerization has shown great promise in the fabrication of three-dimensional (3D) optical waveguides in PDMS without the limit of planar structures. Here we demonstrate a multiphoton laser direct writing process that produces low-loss, ultra-compact waveguides in PDMS. The fabrication employs a self-initiated multiphoton polymerization of phenylacetylene infused in PDMS without additional photoinitiator. The elimination of the photoinitiator results in an excellent refractive index homogeneity and thus a low propagation loss due to scattering, as well as a greater biocompatibility by involving the fewest possible chemicals (monomer only) in the polymerization reaction. Our characterizations show that the waveguides fabricated as such are on average 1.3 µm wide with a refractive index contrast of 0.06 and a propagation loss of 0.03 dB/cm in the spectral band of 650-700 nm. Our technique will enable a broad range of applications spanning from wearable photonics to chip-scale optical interconnects.