We present a new implementation for active galactic nucleus (AGN) feedback through small-scale, ultra-fast winds in the moving-mesh hydrodynamic code AREPO. The wind is injected by prescribing mass, momentum and energy fluxes across a spherical boundary centred on a supermassive black hole according to available constraints for accretion disc winds. After sweeping-up a mass equal to their own, small-scale winds thermalise, powering energy-driven outflows with dynamics, structure and cooling properties in excellent agreement with those of analytic wind solutions. Momentum-driven solutions do not easily occur, because the Compton cooling radius is usually much smaller than the free-expansion radius of the small-scale winds. Through various convergence tests, we demonstrate that our implementation yields wind solutions which are well converged down to the typical resolution achieved in cosmological simulations. We test our model in hydrodynamic simulations of isolated Milky Way - mass galaxies. Above a critical AGN luminosity, initially spherical, small-scale winds power bipolar, energy-driven super-winds that break out of the galactic nucleus, flowing at speeds $> 1000 rm , km , s^{-1}$ out to $sim 10 , rm kpc$. These energy-driven outflows result in moderate, but long-term, reduction in star formation, which becomes more pronounced for higher AGN luminosities and faster small-scale winds. Suppression of star formation proceeds through a rapid mode that involves the removal of the highest-density, nuclear gas and through a slower mode that effectively halts halo gas accretion. Our new implementation makes it possible to model AGN-driven winds in a physically meaningful and validated way in simulations of galaxy evolution, the interstellar medium and black hole accretion flows.