We propose a novel Structure-Preserving Discontinuous Galerkin (SPDG) operator that recovers at the discrete level the algebraic property related to the divergence of the curl of a vector field, which is typically referred to as div-curl problem. A staggered Cartesian grid is adopted in 3D, where the vector field is naturally defined at the corners of the control volume, while its curl is evaluated as a cell-centered quantity. Firstly, the curl operator is rewritten as the divergence of a tensor, hence allowing compatible finite difference schemes to be devised and to be proven to mimic the algebraic div-curl property. Successively, a high order DG divergence operator is built upon integration by parts, so that the structure-preserving finite difference div-curl operator is exactly retrieved for first order discretizations. We further demonstrate that the novel SPDG schemes are capable of obtaining a zero div-curl identity with machine precision from second up to sixth order accuracy. Curl-grad operators follow as a consequence. In a second part, we show the applicability of these SPDG methods by solving the incompressible Navier-Stokes equations written in vortex-stream formulation. This hyperbolic system deals with divergence-free involutions related to the velocity and vorticity field as well as to the stream function, thus it provides an ideal setting for the validation of the novel schemes. A compatible discretization of the numerical viscosity is also proposed in order to maintain the structure-preserving property of the div-curl DG operators even in the presence of artificial or physical dissipative terms. Finally, to overcome the time step restriction dictated by the viscous sub-system, Implicit-Explicit (IMEX) Runge-Kutta time stepping techniques are tailored to handle the SPDG framework. Numerical examples show that the theoretical order of convergence is reached by this new class of methods, and prove the exact preservation of the incompressibility constraint.