We evaluated craniometric sexual dimorphism and ontogenetic (age) variation in invasive Rattus norvegicus and R. rattus from urban and peri-urban areas of Gauteng Province, South Africa, using univariate and multivariate analyses. Two-way analysis of variance (ANOVA), percent contribution of the sum of squares (%SSQs) of each source of variation, principal components analysis (PCA) and unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis showed no sexual dimorphism in both species, however in both species, significant age variation between five age classes based on maxillary molar toothrow cusp eruption and wear was found and the age classes were pooled into juveniles (i.e., individuals of tooth-wear class I), sub-adults (II–III), and adults (IV–V). Few variables showed statistically significant sex-age interaction. The largest %SSQs to the total variance were due to error (i.e., residual ), suggesting that apart from sex, age, and their interaction, there were other components that are responsible for the variation. Our approach may be useful for partitioning the effect of sexual dimorphism and ontogenetic variation in other studies, such as our stable isotope analysis-based trophic ecological studies of Rattus species from urban and peri-urban areas of Gauteng Province, South Africa.