Through Silicon Via (TSV) is a critical enabling technique in three-dimensional integrated circuits (3D ICs). However, it may suffer from many reliability issues. Various fault-tolerance mechanisms have been proposed in literature to improve yield, at the cost of significant area overhead. In this paper, we focus on the structure that uses one spare TSV for a group of original TSVs, and study the optimal assignment of spare TSVs under yield and timing constraints to minimize the total area overhead. We show that such problem can be modeled through constrained graph decomposition. An efficient heuristic is further developed to address this problem. Experimental results show that under the same yield and timing constraints, our heuristic can reduce the area overhead induced by the fault-tolerance mechanisms by up to 38%, compared with a seemingly more intuitive nearest-neighbor based heuristic.