This paper deals with the estimation of structural modal parameters of long-span bridges from their recorded wind-excited response, by separating structural properties from aeroelastic effects using information on the incoming wind velocity. Specific attention is devoted to structural damping ratios, as their accurate estimations are of crucial importance in bridge engineering. However, uncertainties affecting damping ratios estimates often complicate any attempt towards their accurate assessment. More importantly, in the case of long-span bridges, aerodynamic damping often hides the actual structural one, even at low wind velocities. In this paper, the use of a data-driven stochastic subspace approach, specifically conceived to eliminate, as much as possible, analyst's arbitrariness and to deal with the non-whiteness of the wind excitation, is proposed for system identification. Structural properties are then separated from aeroelastic effects via nonlinear regressions of the modal parameter estimates at different mean wind velocities. Application of this technique to field measurements and numerically simulated buffeting response data referred to a real suspension bridge is finally presented, showing its effectiveness for separating structural from aerodynamic damping in practical case studies.