A new method for solving the time-dependent two-center Dirac equation is developed. The approach is based on the using of the finite basis of cubic Hermite splines on a three-dimensional lattice in the coordinate space. The relativistic calculations of the excitation and charge-transfer probabilities in the low-energy U91+ (1s)–U92+ collisions in two and three dimensional approaches are performed. The obtained results are compared with our previous calculations employing the Dirac-Sturm basis sets [I.I. Tupitsyn et al., Phys. Rev. A 82, 042701 (2010)]. The role of the negative-energy Dirac spectrum is investigated within the monopole approximation.