From the wiki article on color vision as an illustration of how photons are absorbed:
Perception of color begins with specialized retinal cells containing pigments with different spectral sensitivities, known as cone cells. In humans, there are three types of cones sensitive to three different spectra, resulting in trichromatic color vision.
Each individual cone contains pigments composed of opsin apoprotein, which is covalently linked to either 11-cis-hydroretinal or more rarely 11-cis-dehydroretinal.
So it is molecules with different absorption spectra that absorb the optical photons and start the sequence of giving a signal to the brain. It is not a simple matter and belongs more to biology than to physics. The physics part is just that the photon hits a molecule and raises an electron to a higher level which generates a series of reactions that finally register in the brain.