We demonstrate that the three-dimensional Skyrmion, which has remained elusive so far, spontaneously appears as the ground state of SU(2) symmetric Bose-Einstein condensates coupled with a non-Abelian gauge field. The gauge field is a three-dimensional analogue of the Rashba spin-orbit coupling. Upon squashing the SO(3) symmetric gauge field to one- or two-dimensional shapes, we find that the ground state continuously undergoes a change from a three-dimensional to a one- or two-dimensional Skyrmion, which is identified by estimating winding numbers and helicity. All of the emerged Skyrmions are physically understandable with the concept of the helical modulation in a unified way. These topological objects might potentially be realizable in two-component Bose-Einstein condensates experimentally.