Advanced Persistent Threats (APTs) are stealthy customized attacks by intelligent adversaries. This paper deals with the detection of APTs that infiltrate cyber systems and compromise specifically targeted data and/or infrastructures. Dynamic information flow tracking is an information trace-based detection mechanism against APTs that taints suspicious information flows in the system and generates security analysis for unauthorized use of tainted data. In this paper, we develop an analytical model for resource-efficient detection of APTs using an information flow tracking game. The game is a nonzero-sum, turn-based, stochastic game with asymmetric information as the defender cannot distinguish whether an incoming flow is malicious or benign and hence has only partial state observation. We analyze equilibrium of the game and prove that a Nash equilibrium is given by a solution to the minimum capacity cut set problem on a flow-network derived from the system, where the edge capacities are obtained from the cost of performing security analysis. Finally, we implement our algorithm on the real-world dataset for a data exfiltration attack augmented with false-negative and false-positive rates and compute an optimal defender strategy.