In this paper, we present the third data release (DR3) of the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS). We identify likely near- infrared counterparts to submillimetre sources in the South Galactic Pole (SGP) field using the VISTA VIKING survey. We search for the most probable counterparts within 15 arcsec of each Herschel source using a probability measure based on the ratio between the likelihood the true counterpart is found close to the submillimetre source and the likelihood that an unrelated object is found in the same location. For 110374 (57.0 per cent) sources, we find galaxies on the near-infrared images where the probability that the galaxy is associated to the source is greater than 0.8. We estimate the false identification rate to be 4.8 per cent, with a probability that the source has an associated counterpart on the VIKING images of 0.835 +/- 0.009. We investigate the effects of gravitational lensing and present 41 (0.14 deg^-2^) candidate lensed systems with observed flux densities >100 mJy at 500 {mu}m. We include in the data release a probability that each source is gravitationally lensed and discover an additional 5923 sources below 100 mJy that have a probability greater than 0.94 of being gravitationally lensed. We estimate that ~400-1000 sources have multiple true identifications in VIKING based on the similarity of redshift estimates for multiple counterparts close to a Herschel source. The data described in this paper can be found at the H-ATLAS website.