The interaction between the supermassive black hole at the center of the Milky Way, Sagittarius A$^*$, and its accretion disk, occasionally produces high energy flares seen in X-ray, infrared and radio. One mechanism for observed flares is the formation of compact bright regions that appear within the accretion disk and close to the event horizon. Understanding these flares can provide a window into black hole accretion processes. Although sophisticated simulations predict the formation of these flares, their structure has yet to be recovered by observations. Here we show the first three-dimensional (3D) reconstruction of an emission flare in orbit recovered from ALMA light curves observed on April 11, 2017. Our recovery results show compact bright regions at a distance of roughly 6 times the event horizon. Moreover, our recovery suggests a clockwise rotation in a low-inclination orbital plane, a result consistent with prior studies by EHT and GRAVITY collaborations. To recover this emission structure we solve a highly ill-posed tomography problem by integrating a neural 3D representation (an emergent artificial intelligence approach for 3D reconstruction) with a gravitational model for black holes. Although the recovered 3D structure is subject, and sometimes sensitive, to the model assumptions, under physically motivated choices we find that our results are stable and our approach is successful on simulated data. We anticipate that in the future, this approach could be used to analyze a richer collection of time-series data that could shed light on the mechanisms governing black hole and plasma dynamics.