We present a theory that incorporates the vibrational degrees of freedom in a high-order harmonic generation (HHG) process with ultrashort intense laser pulses. In this model, laser-induced time-dependent transition dipoles for each fixed molecular geometry are added coherently, weighted by the laser-driven time-dependent nuclear wave packet distribution. We show that the nuclear distribution can be strongly modified by the HHG driving laser. The validity of this model is first checked against results from the numerical solution of the time-dependent Schrödinger equation for a simple model system. We show that in combination with the established quantitative rescattering theory this model is able to reproduce the time-resolved pump-probe HHG spectra of N(2)O(4) reported by Li et al. [Science 322, 1207 (2008)].