Using density functional theory simulations, we examine the electronic structure of an isolated monovacancy defect in graphene under symmetry-breaking deformation. Results show that the defect experiences a second-order Jahn–Teller reconstruction at a critical strain of 1.7%. It stabilizes the orientation of the JT bond relative to the loading direction and breaks the threefold degeneracy of the defect structure. We call it Jahn–Teller re-reconstruction (JTRR), and it is mechanically reversible. The reversibility and stabilization of the orientation depend on the direction cosine between the JT bond and the loading direction. Also, a change in the loading direction by 90° can change the orientation of the JT bond by 120°. An atomic-scale analysis suggests that the maximum bond force arising from “the derivative of the kinetic energy of electrons” defines the critical strain. JTRR alters the electron occupation in the individual electronic orbitals at the defect site. The electronic charge redistribution and the density of states at the defective sites reveal that the pz orbitals dominate the reconstruction process. Furthermore, JTRR changes the magnitude of the magnetic moment at the defective site from 1.36 μB to 1.22 μB. This unravels a new way of controlling the magnetic behavior of monovacancy by applying symmetry-breaking mechanical strain. Results also show that passivation of the dangling bond can subside or eliminate the reconstruction process depending on the number of valence electrons available in the passivating atom.