A major unsolved puzzle in cuprate superconductivity is that, despite accumulated evidence of more conventional normal state properties over the last 30 years, the superconducting $T_c$ of the overdoped cuprates seems to be still controlled by phase coherence rather than the Cooper pair formation. So far, a microscopic understanding of this unexpected behavior is lacking. Here we report angle-resolved photoemission, magnetic and thermodynamic evidence that Cooper pairs form at temperatures more than 30% above $T_c$ in overdoped metallic Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ (Bi-2212). More importantly, our data lead to a microscopic understanding where the phase fluctuation is enhanced by the flat dispersion near the Brillouin zone boundary. This proposal is tested by a sign-problem free quantum Monte Carlo simulation. Such a microscopic mechanism is likely to find applications in other flat band superconductors, such as twisted bilayer-bilayer graphene and NdNiO$_2$