This paper proposes an incentive-based cooperative payoff design method to accommodate faults in weakly acyclic games, where the payoff functions of normal players are designed such that all players’ optimal payoffs are recovered into an admissible level. Besides, the stochastically stable Nash equilibrium (SSNE) is regarded as the optimal state to avoid some inefficient Nash equilibria. Firstly, without cooperation among players, the effect of faults on SSNE and the optimal payoff is analyzed deeply. Further, the conditions of fault accommodation are discussed under the proposed cooperative fault tolerance method, based on which an algorithm is designed to calculate the feasible incentive. Secondly, with cooperation among players, the effect of faults is analyzed again in special weakly acyclic games, namely potential games, and the simpler conditions of fault accommodation are provided. Finally, two examples of frequency assignment in distributed systems and power management in sensor networks illustrate the effectiveness of the proposed methods.