We introduce a fast and efficient variational framework for Simultaneous Registration and Segmentation (SRS) applicable to a wide variety of image sequences. We demonstrate that a dense correspondence map (between consecutive frames) can be reconstructed correctly even in the presence of partial occlusion, shading, and reflections. The errors are efficiently handled by exploiting their sparse nature. In addition, the segmentation functional is reformulated using a dual Rudin-Osher-Fatemi (ROF) model for fast implementation. Moreover, nonparametric shape prior terms that are suited for this dual-ROF model are proposed. The efficacy of the proposed method is validated with extensive experiments on both indoor, outdoor natural and biological image sequences, demonstrating the higher accuracy and efficiency compared to various state-of-the-art methods.