We present SCExAO/CHARIS 1.1–2.4 μm integral field direct spectroscopy of the young HIP 79124 triple system. HIP 79124 is a member of the Scorpius-Centaurus association, consisting of an A0V primary with two low-mass companions at a projected separation of < 1″. Thanks to the high quality wavefront corrections provided by SCExAO, both companions are decisively detected without the employment of any PSF-subtraction algorithm to eliminate quasi-static noise. The spectrum of the outer C object is very well matched by Upper Scorpius M4 ± 0.5 standard spectra, with a T_eff = 2945 ± 100 K and a mass of ∼350 M_Jup. HIP 79124 B is detected at a separation of only 180 mas in a highly-correlated noise regime, and it falls in the spectral range M6 ± 0.5 with T_eff = 2840 ± 190 K and ∼100 M_Jup. Previous studies of stellar populations in Sco-Cen have highlighted a discrepancy in isochronal ages between the lower-mass and higher-mass populations. This could be explained either by an age spread in the region, or by conventional isochronal models failing to reproduce the evolution of low-mass stars. The HIP 79124 system should be coeval, and therefore it provides an ideal laboratory to test these scenarios. We place the three components in a color–magnitude diagram and find that the models predict a younger age for the two low-mass companions (∼3 Myr) than for the primary star (∼6 Myr). These results imply that the omission of magnetic effects in conventional isochronal models inhibit them from reproducing early low-mass stellar evolution, which is further supported by the fact that new models that include such effects provide more consistent ages in the HIP 79124 system.