The discrete tori are graph analogues of the real tori, which are defined by the Cayley graphs of a finite product of finite cyclic groups. In this paper, using the theory of the heat kernel on the discrete tori established by Chinta, Jorgenson and Karlsson, we derive an explicit prime geodesic theorem for the discrete tori, which is not an asymptotic formula. To describe the formula, we need generalizations of the classical Jacobi polynomials, which are defined by the Lauricella multivariable hypergeometric function of type C.