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The cuprate high-temperature superconductors exhibit many unexplained electronic phases, but it was often thought that the superconductivity at sufficiently high doping is governed by conventional mean-field Bardeen-Cooper-Schrieffer (BCS) theory[1]. However, recent measurements show that the number of paired electrons (the superfluid density) vanishes when the transition temperature Tc goes to zero[2], in contradiction to expectation from BCS theory. The origin of this anomalous vanishing is unknown. Our scanning tunneling spectroscopy measurements in the overdoped regime of the (Pb,Bi)2Sr2CuO6+{\delta} high-temperature superconductor show that it is due to the emergence of puddled superconductivity, featuring nanoscale superconducting islands in a metallic matrix[3,4]. Our measurements further reveal that this puddling is driven by gap filling, while the gap itself persists beyond the breakdown of superconductivity. The important implication is that it is not a diminishing pairing interaction that causes the breakdown of superconductivity. Unexpectedly, the measured gap-to-filling correlation also reveals that pair-breaking by disorder does not play a dominant role and that the mechanism of superconductivity in overdoped cuprate superconductors is qualitatively different from conventional mean-field theory.