This paper investigates a dual-channel supply chain (SC) composed of a manufacturer and retailer in which the manufacturer confronts random yield issues. Since supply uncertainty may lead to a production shortage, the manufacturer faces the problem of allocating the products to traditional/online channels. To address this problem, a novel product-allocation policy is developed in which the limited supply is allocated to traditional and online channels under a flexible strategy called “targeted capacity allocation”. In order to coordinate the proposed decentralized channel, a two-part tariff contract is suggested. Furthermore, opening a direct channel besides brick-and-mortar stores is discussed through analytical results. Then, the effectiveness of the targeted capacity allocation policy is investigated by comparing the results of the current model with a case, in which, the same policy is not applied. By doing so, some interesting managerial insights on the merit of applying the capacity allocation policy in managing dual-channel SCs under yield uncertainty are revealed. Finally, numerical analysis shows that the proposed contract can perfectly coordinate the SC and achieve the Pareto improving solution for both partners.