Gold–palladium nanoparticles with an average size of 3.5 nm and controlled compositions were grown on rutile titania nanorods using pulsed laser deposition. The structural properties of the as-synthesized nanoparticles and their interface with the oxide support were studied at the atomic scale using aberration-corrected transmission electron microscopy (TEM). High resolution TEM imaging showed that both polycrystalline Au–Pd particles with droplet morphology and single-crystalline particles with truncated octahedron morphology were stabilized on the nanorods during laser deposition depending on the degree of epitaxy between the nanoparticles and the oxide support. By analyzing the single-crystalline particles formed in the presence of a strong epitaxy, 11 epitaxial relationships between the Au–Pd nanoparticles and their support were identified with the two dominant ones being: Au–Pd (111) [101] // r-TiO2(110) [11̅1̅] and Au–Pd (100) [101] // r-TiO2 (110) [11̅0]. Catalytic testing of the bimetallic titania-supported Au–Pd nanoparticles in the partial hydrogenation of 1,3-butadiene showed that they were both active and selective for this reaction. An increase in the catalytic stability with the gold content was evidenced.