The characterization and evaluation of the recent status of biodiversity in Southern Africa’s Savannas is a major prerequisite for suitable and sustainable land management and conservation purposes. This paper presents an integrated concept for vegetation type mapping in a dry savanna ecosystem based on local scale in-situ botanical survey data with high resolution (Landsat) and coarse resolution (MODIS) satellite time series. In this context, a semi-automated training database generation procedure using object-oriented image segmentation techniques is introduced. A tree-based Random Forest classifier was used for mapping vegetation type associations in the Kalahari of NE Namibia based on inter-annual intensity- and phenology-related time series metrics. The utilization of long-term inter-annual temporal metrics delivered the best classification accuracies (Kappa = 0.93) compared with classifications based on seasonal feature sets. The relationship between annual classification accuracies and bi-annual precipitation sums was conducted using data from the Tropical Rainfall Measuring Mission (TRMM). Increased error rates occurred in years with high rainfall rates compared to dry rainy seasons. The variable importance was analyzed and showed high-rank positions for features of the Enhanced Vegetation Index (EVI) and the blue and middle infrared bands, indicating that soil reflectance was crucial information for an accurate spectral discrimination of Kalahari vegetation types. Time series features related to reflectance intensity obtained increased rank-positions compared to phenology-related metrics.