In his 1962 article "A unique decomposition theorem for 3-manifolds", Milnor is actually interested in the unicity of a prime decomposition. For the existence, the method is very natural: if you find an irreducible sphere, you cut the manifold along it and obtain a decomposition $M = M_1 \sharp M_2$, and you do it again with each factor, and so on.
Of course, the hard part is now to prove that this process terminates after a finite number of steps. For that, Milnor refers to Kneser but remarks that "if one assumes the Poincaré hypothesis then there is a much easier proof. Define $\rho(M)$ as the smallest number of generators for the fundamental group of M. It follows from the Gruško-Neumann theorem that $\rho(M_1\sharp M_2) = \rho(M_1) + \rho(M_2)$. Hence if $M\simeq M_1 \sharp \cdots \sharp M_k$ with $k > \rho(M)$ then some $M_i$ must satisfy $\rho(M_i)=0$, and hence must be isomorphic to $S^3$."