We propose formulating the finite-horizon stochastic optimal control problem for colloidal self-assembly in the space of probability density functions (PDFs) of the underlying state variables (namely, order parameters). The control objective is formulated in terms of steering the state PDFs from a prescribed initial probability measure towards a prescribed terminal probability measure with minimum control effort. For specificity, we use a univariate stochastic state model from the literature. Both the analysis and the computational steps for control synthesis as developed in this paper generalize for multivariate stochastic state dynamics given by generic nonlinear in state and non-affine in control models. We derive the conditions of optimality for the associated optimal control problem. This derivation yields a system of three coupled partial differential equations together with the boundary conditions at the initial and terminal times. The resulting system is a generalized instance of the so-called Schrödinger bridge problem. We then determine the optimal control policy by training a physics-informed deep neural network, where the "physics" are the derived conditions of optimality. The performance of the proposed solution is demonstrated via numerical simulations on a benchmark colloidal self-assembly problem.