The global ocean overturning circulation, critically dependent on the global density stratification, plays a central role in regulating climate evolution. While it is well known that the global stratification profile exhibits a strong dependence to Southern Ocean dynamics and in particular to wind and buoyancy forcing, we demonstrate here that the stratification is also acutely sensitive to the mesoscale eddy energy dissipation timescale. Within the context of a global ocean circulation model with an energy constrained mesoscale eddy parameterization, it is shown that modest variations in the eddy energy dissipation timescale lead to significant variations in key metrics relating to ocean circulation, namely the Antarctic Circumpolar Current transport, Atlantic Meridional Overturning Circulation strength, and global ocean heat content, over long timescales. The results highlight a need to constrain uncertainties associated with eddy energy dissipation for climate model projections over centennial timescales and also for paleoclimate simulations over millennial timescales.