Software-Defined Networking (SDN) can be applied for managing application flows dynamically by a logically centralized SDN controller and SDN switches. Because one SDN switch can support just a few thousand forwarding rule installations per second, it is a barrier to dynamic and scalable application flow management. For this reason, it is essential to reduce the number of application flows if they are to be successfully managed. Nowadays, since much attention has been paid to developing a network service that reduces application delay, the allowable delay of application flows has become an important factor. However, there has been no work on minimizing the number of flows while satisfying end-to-end delay of flows. In this paper, we propose a method that can aggregate flows and minimize the number flows in a network while ensuring all flows satisfy their allowable delay in accordance with QoS or SLA. Since the problem is classified as NP-hard, we propose a heuristic algorithm. We compared the aggregation effect of the proposed method, simple aggregation method and optimal solution by simulation. In addition, we clarify the characteristics of the proposed method by performing simulations with various parameter settings. The results show that the proposed method decreases the number of rules than comparative aggregation method and has very shorter computational time than optimal solution.