A reduced-order model of finite periodic structures with absorbing boundary conditions (ABCs) and localized time-dependent excitations is proposed. 1D-periodic structures whose cells can represent any 2D or 3D arbitrary substructures are considered. The key steps for modeling an ABC in the time domain are: (i) expression of the impedance matrix with the wave finite element (WFE) method; (ii) partial rational decomposition of the impedance matrix; (iii) introduction of vectors of supplementary variables to describe the ABC in the time domain. In this paper, a model reduction approach is proposed to speed up the computation of the ABCs. The focus is on the reduction of the number of internal degrees of freedom of substructures, and the reduction of the number of degrees of freedom at the substructure interfaces. The approach allows the consideration of complex substructures with large FE models, and the computation of the time response of periodic structures at a low computational cost. Numerical experiments are carried out to highlight the relevance of the proposed approach. Specifically, the analysis of a metamaterial structure containing nonlinear resonant substructures is carried out with the proposed approach. Results show that, when compared to the linear case, band gaps in periodic structures with nonlinear substructures can be significantly improved.