Understanding the connection between a material’s microscopic network topology and its macroscopic properties is a fundamental open challenge across a wide range of physical systems. Here, we investigate the elasticity of DNA nanostar hydrogels – a model system for networks with limited valence – by coupling rheology measurements, confocal imaging and molecular dynamics simulations. We discover that these networks display a large degree of interpenetration and that loops within the network are topologically linked, forming a percolating network-within-network structure. Strikingly, we discover that the onset of topological links between shortest loops fully determines the elasticity of these physical gels. We thus argue that the elasticity of limited valence gels is not dictated by their fractal microstructure, but by the topology of looped motifs. Our findings highlight the emergence of “topological elasticity” as a previously overlooked mechanism in generic network-forming liquids and physical gels and will inspire the design of topologically-controllable material behaviours.