Changes in the structural association of skeletal traits are crucial to the evolution of novel forms and functions. In vertebrates, such rearrangements often occur gradually and may precede or coincide with the functional activation of skeletal traits. To illustrate this process, we examined the ontogeny of African hinge-back tortoises (Kinixys spp.). Kinixys species feature a moveable “hinge” on the dorsal shell (carapace) that enables shell closure (kinesis) when the hind limbs are withdrawn. This hinge, however, is absent in juveniles. Herein, we describe how this unusual phenotype arises via alterations in the tissue configuration and shape of the carapace. The ontogenetic repatterning of osseous and keratinous tissue coincided with shifts in morphological integration and the establishment of anterior (static) and posterior (kinetic) carapacial modules. Based on ex vivo skeletal movement and raw anatomy, we propose that Kinixys employs a “sliding hinge” shell-closing system that overcomes thoracic rigidity and enhances the protective capacity of the carapace. Universal properties of the vertebrate skeleton, such as plasticity, modularity, and secondary maturation processes, contributed to adaptive evolutionary change in Kinixys. We discuss a hypothetical model to explain the delayed emergence of skeletal traits and its relevance to the origins of novel form-to-function relationships.