The configurational information in sentences of a free word order language such as Sanskrit is of limited use. Thus, the context of the entire sentence will be desirable even for basic processing tasks such as word segmentation. We propose a structured prediction framework that jointly solves the word segmentation and morphological tagging tasks in Sanskrit. We build an energy based model where we adopt approaches generally employed in graph based parsing techniques (McDonald et al., 2005a; Carreras, 2007). Our model outperforms the state of the art with an F-Score of 96.92 (percentage improvement of 7.06%) while using less than one tenth of the task-specific training data. We find that the use of a graph based approach instead of a traditional lattice-based sequential labelling approach leads to a percentage gain of 12.6% in F-Score for the segmentation task.