We introduce the concept of pairwise tomography networks to characterize quantum properties in many-body systems and demonstrate an efficient protocol to measure them experimentally. Pairwise tomography networks are generators of multiplex networks where each layer represents the graph of a relevant quantifier, such as, e.g., concurrence, quantum discord, purity, quantum mutual information, or classical correlations. We propose a measurement scheme to perform two-qubit tomography of all pairs showing exponential improvement in the number of qubits N with respect to previously existing methods. We illustrate the usefulness of our approach by means of several examples revealing its potential impact to quantum computation, communication, and simulation. We perform a proof-of-principle experiment demonstrating pairwise tomography networks of W states on IBM Q devices.