Regional maps of vegetation structure are necessary for delineating species habitats and for supporting conservation and ecological analyses. A systematic approach that can discriminate a wide range of meaningful and detailed vegetation classes is still lacking for neotropical savannas. Detailed vegetation mapping of savannas is challenged by seasonal vegetation dynamics and substantial heterogeneity in vegetation structure and composition, but fine spatial resolution imagery (<10 m) can improve map accuracy in these heterogeneous landscapes. Traditional pixel-based classification methods have proven problematic for fine spatial resolution data due to increased within-class spectral variability. Geographic Object-Based Image Analysis (GEOBIA) is a robust alternative method to overcome these issues. We developed a systematic GEOBIA framework accounting for both spectral and spatial features to map Cerrado structural types at 5-m resolution. This two-step framework begins with image segmentation and a Random Forest land cover classification based on spectral information, followed by spatial contextual and topological rules developed in a systematic manner in a GEOBIA knowledge-based approach. Spatial rules were defined a priori based on descriptions of environmental characteristics of 11 different physiognomic types and their relationships to edaphic conditions represented by stream networks (hydrography), topography, and substrate. The Random Forest land cover classification resulted in 10 land cover classes with 84.4% overall map accuracy and was able to map 7 of the 11 vegetation classes. The second step resulted in mapping 13 classes with 87.6% overall accuracy, of which all 11 vegetation classes were identified. Our results demonstrate that 5-m spatial resolution imagery is adequate for mapping land cover types of savanna structural elements. The GEOBIA framework, however, is essential for refining land cover categories to ecological classes (physiognomic types), leading to a higher number of vegetation classes while improving overall accuracy.