This paper proposes an automated pairing approach for configuration selection of decentralized controllers which considers system uncertainties. Following the Relative Interaction Array (RIA) pairing rules, the optimal control configuration, i.e. the configuration that fits best the pairing rules, is obtained automatically by formulating the control configuration selection problem as an Assignment Problem (AP). In this AP, the associated costs related to each input-output pairing are given by the RIA coefficients. The Push-Pull algorithm is used to solve the AP for the nominal system and to obtain the set of costs for which the resulting configuration remains optimal, also called the perturbation set. The introduction of uncertainty bounds on the RIA-based costs enables the testing of the possible violation of the optimality conditions. Examples to illustrate the proposed approach for a 3×3 system and 4×4 gasifier plant are given.