Combining a semiclassical analysis with exact diagonalizations, we show that the ground state of the SU(3) Heisenberg model on the square lattice develops three-sublattice long-range order. This surprising pattern for a bipartite lattice with only nearest-neighbor interactions is shown to be the consequence of a subtle quantum order-by-disorder mechanism. By contrast, thermal fluctuations favor two-sublattice configurations via entropic selection. These results are shown to extend to the cubic lattice, and experimental implications for the Mott-insulating states of three-flavor fermionic atoms in optical lattices are discussed.