Along tectonically active margins, the difference in elevations between global sea levels during highstands and uplifted marine terraces is a function of both tectonics and glacial-isostatic adjustment (GIA). However, disentangling the relative influence of these two processes remains a challenge for those trying to gain insights into either process. In this study, we outline a strategy for isolating the tectonic contribution to marine isotope stage (MIS) 5e and 5a marine terrace elevations for the southern California coast by determining the cosmogenic radionuclide burial age and elevation of the early Pleistocene (1.48 ± 0.17 Ma) Clairemont Terrace in San Diego. Using this older terrace as a datum for calculating tectonic uplift rate provides a much longer time period to average out uncertainties in past local or relative sea levels (RSL) that arise from ambiguities in GIA parameters and global meltwater volumes. The assumption of constant uplift rates is warranted for this portion of the California coast given its relatively simple tectonic setting on the rift flank of the Salton Trough. From this approach, we determine an average uplift rate of 0.066 ± 0.020 mm/yr or 0.055 ± 0.013 mm/yr, depending on the RSL model used for the time of the Clairemont Terrace formation, for much of the San Diego coastline. Correcting for this tectonic uplift rate leaves an estimate of 15.1 + 2.6/-3.1 m (16.4 + 1.9/-2.6 m) and 4.8 ± 1.9 m (5.6 ± 1.5 m) for RSL during MIS5e and MIS5a, respectively. These new estimates of MIS5e and MIS5a sea levels along the southern California coast provide important constraints on GIA parameters and former ocean and ice volumes.