Based on visuo-tactile stimulation, the rubber hand illusion induces a sense of ownership for a dummy hand. Manipulating the visibility of the dummy hand during the stimulation influences cognitive aspects of the illusion, suggesting that the related brain activity may be influenced too. To test this, we analyzed brain activity (fMRI), subjective ratings, and skin conductance from 45 neurotypical participants undergoing a modified rubber hand illusion protocol where we manipulated the visibility (high, medium, and low) of a virtual hand, not the brush (virtual hand illusion; VHI). To further investigate the impact of visibility manipulations on VHI-related secondary effects (i.e. vicarious somatosensation), we recorded brain activity and skin conductance during a vicarious pain protocol (observation of painful stimulations of the virtual hand) that occurred after the VHI procedure. Results showed that, during both the VHI and vicarious pain periods, the activity of distinct visual, somatosensory, and motor brain regions was modulated by (i) visibility manipulations, (ii) coherence between visual and tactile stimulation, and (iii) time of visuo-tactile stimulation. Accordingly, embodiment-related subjective ratings of the perceived illusion were specifically influenced by visibility manipulations. These findings suggest that visibility modifications can impact the neural and cognitive effects of illusory body ownership, in that when visibility decreases the illusion is perceived as weaker and the brain activity in visual, motor, and somatosensory regions is overall lower. We interpret this evidence as a sign of the weight of vision on embodiment processes, in that the cortical and subjective aspects of illusory body ownership are weakened by a degradation of visual input during the induction of the illusion.