Two-dimensional direction-of-arrival (2D-DOA) estimation for uniform rectangular array (URA) is a canonical problem with numerous applications, e.g., wireless communications, sonar and radar systems. The conventional 2D-DOA estimators usually are derived with the assumption of ideal arrays. However, in practice, the arrays may not be well calibrated and suffer from unknown mutual coupling. Using the conventional estimators may lead to low accuracy estimation and high computational complexity in the condition of large number of array elements. In this paper, a novel real-valued parallel factor (PARAFAC) decomposition algorithm is proposed to tackle this problem. The proposed algorithm has better angle estimation performance than the multiple signal classification (MUSIC) algorithm, estimation of signal parameters via rotational invariance techniques (ESPRIT) algorithm and conventional PARAFAC algorithm. But it has lower complexity than MUSIC algorithm. Moreover, the proposed algorithm can obtain automatically paired 2D-DOA estimation, and it is suitable to coherent or closely spaced signals and can eliminate the mutual coupling. Simulation results verify the effectiveness of the proposed algorithm.