A method for correcting motion-induced phase errors in diffusion-weighted k-space data acquired with a magnetic resonance imaging (MRI) system is provided. The MRI system is directed to acquire the following data from an imaging volume: three-dimensional diffusion-weighted k-space data, three-dimensional diffusion-weighted navigator data, three-dimensional non-diffusion-weighted k-space data, and three-dimensional non-diffusion-weighted navigator data. Initial estimates of k-space shift values and a constant phase offset value are calculated using the three-dimensional diffusion-weighted navigator data and the three-dimensional non-diffusion-weighted navigator data. These initial k-space shift values and constant phase offset value are then updated by iteratively minimizing a cost function that relates the phase of the diffusion-weighted k-space data to the phase of the non-diffusion-weighted k-space data, as shifted by the initial k-space shift values and constant phase offset value. The diffusion-weighted k-space data is then corrected for motion-induced phase errors using the updated k-space shift values and constant phase offset value.