The São Francisco Craton and its adjacent units show several main structural features. One of the most intriguing structures is the Pirapora Aulacogen, the largest Proterozoic rift structure preserved in the São Francisco Basin that records the Gondwana breakup event. This work used gravity and magnetic data to estimate geological structures within Pirapora Aulacogen, located on the eastern part of São Francisco Craton. The integrated geophysical and geological data analysis allowed us to increase geophysical information on this area by the magnetic and gravity signatures. Spectral analysis of the gravity and magnetic data revealed the depth of the sources of structures hosted basement. From potential field data, the Analytic Signal Amplitude (ASA), the Vertical Derivative (VDR), Tilt Derivative (TDR), and the Total Horizontal Derivative (THDR) products, it was possible to identify important signatures, as well as to delimit main structures. The Euler deconvolution technique provided estimates of the locations and depths of magnetic and gravity sources. It revealed important structures in the sedimentary cover and also structures responsible for the basement uplift. Modeling these data was performed in a strategic section of the study area to create a geological-geophysical model representing the subsurface geological features. The forward modeling and the inversion of the gravity and magnetic data generated from conventional susceptibility and the Magnetization Vector Inversion (MVI) were correlated to create a geophysical-geological model that presents the main geological features. The difference between conventional susceptibility and MVI results confirmed a strong magnetization remanence in the area. The largest amplitudes of the local gravitational field, also observed in the gravity inversion, are interpreted due to the basement uplift in the mountain regions: Serra do Cabral and Água Fria. The main structures revealed in the section are associated with grabens and horsts, describes as reactivated structures that controlled São Francisco Basin sedimentation.