The evolution of semi-independent modules is hypothesized to underlie the functional diversification of serially repeating (metameric) structures. The mammal vertebral column is a classic example of a metameric structure that is both modular, with well-defined morphological regions, and functionally differentiated. How the evolution of regions is related to their functional differentiation in the forerunners of mammals remains unclear. Here we gathered morphometric and biomechanical data on the presacral vertebrae of two extant species that bracket the synapsid-mammal transition and use the relationship between form and function to predict functional differentiation in extinct non-mammalian synapsids. The origin of vertebral functional diversity does not correlate with the evolution of new regions but appears late in synapsid evolution. This decoupling of regions from functional diversity implies that an adaptive trigger is needed to exploit existing modularity. We propose that the release of axial respiratory constraints, combined with selection for novel mammalian behaviours in Late Triassic cynodonts, drove the functional divergence of pre-existing morphological regions.