A symplectic polarity of a building Δ of type E6 is a polarity whose fixed point structure is a building of type F4 containing residues isomorphic to symplectic polar spaces (i.e., so-called split buildings of type F4). In this paper, we show in a geometric way that every building of type E6 contains, up to conjugacy, a unique class of symplectic polarities. We also show that the natural point-line geometry of each split building of type F4 fully embedded in the natural point-line geometry of Δ arises from a symplectic polarity.