We propose a variational method for segmenting image sequences into spatio-temporal domains of homogeneous motion. To this end, we formulate the problem of motion estimation in the framework of Bayesian inference, using a prior which favors domain boundaries of minimal surface area. We derive a cost functional which depends on a surface in space-time separating a set of motion regions, as well as a set of vectors modeling the motion in each region. We propose a multiphase level set formulation of this functional, in which the surface and the motion regions are represented implicitly by a vector-valued level set function. Joint minimization of the proposed functional results in an eigenvalue problem for the motion model of each region and in a gradient descent evolution for the separating interface. Numerical results on real-world sequences demonstrate that minimization of a single cost functional generates a segmentation of space-time into multiple motion regions.