We present a loosely coupled, partitioned scheme for solving fluid-structure interaction (FSI) problems with the Navier slip boundary condition. The fluid flow is modeled by the Navier-Stokes equations for an incompressible, viscous fluid, interacting with a thin elastic structure modeled by the membrane or Koiter shell type equations. The fluid and structure are coupled via two sets of coupling conditions: a dynamic coupling condition describing balance of forces, and a kinematic coupling condition describing fluid slipping tangentially to the moving fluid-structure interface, with no penetration in the normal direction. Problems of this type arise in, e.g., FSI with hydrophobic structures or surfaces treated with a no-stick coating, and in biologic FSI involving rough surfaces of elastic tissues or tissue scaffolds. We propose a novel, efficient partitioned scheme where the fluid sub-problem is solved separately from the structure sub-problem, and there is no need for sub-iterations at every time step to achieve stability, convergence, and its first-order accuracy. We derive energy estimates, which prove that the proposed scheme is unconditionally stable for the corresponding linear problem. Moreover, we present convergence analysis and show that under a time-step condition, the method is first-order accurate in time and optimally convergent in space for a Finite Element Method-based spatial discretization. The theoretical rates of convergence in time are confirmed numerically on an example with an explicit solution using the method of manufactured solutions, and on a benchmark problem describing propagation of a pressure pulse in a two-dimensional channel. The effects of the slip rate and fluid viscosity on the FSI solution are numerically investigated in two additional examples: a 2D cylindrical FSI example for which an exact Navier slip Poiseuille-type solution is found and used for comparison, and a squeezed ketchup bottle example with gravity enhanced flow. We show that the Navier-slip boundary condition increases the outflow mass flow rate by 21% for a bottle angled at 45 degrees pointing downward, in the direction of gravity.