Aseismic deformation has been suggested as a mechanism to release the accumulated strain in rifts. However, the fraction and the spatial distribution of the aseismic strain are poorly constrained during amagmatic episodes. Using Sentinel-1 interferograms, we identify the surface deformation associated with the 2014 Mw5.2 Karonga earthquake, Malawi, and perform inversions for fault geometry. We also analyze aftershocks and find a variety of source mechanisms within short timescales. A significant discrepancy in the earthquake depth determined by geodesy (3–6 km) and seismology (11–13 km) exists, although both methods indicate Mw5.2. We propose that the surface deformation is caused by aseismic slip from a shallow depth. This vertical partitioning from seismic to aseismic strain is accommodated by intersecting dilatational faults in the shallow upper crust and sedimentary basin, highlighting the importance of considering aseismic deformation in active tectonics and time-averaged strain patterns, even in rifts with little volcanism.