A drastic pruning strategy was developed to eradicate the fungal disease black rot (Guignardia bidwellii), which is exotic in Australia, from grapevines, while minimizing the economic cost of returning an affected vineyard to its previous quality and production levels. The protocol involved cutting off vines at the top of the trunk, removing debris from the ground beneath and between vines, mulching the vineyard floor, removing low watershoots during vine regrowth and applying a targeted fungicide programme. The protocol was initially evaluated and consequently modified in Australia using an endemic grapevine disease, black spot or anthracnose (Elsinoe ampelina), as an analogous model system. Then, it was validated in a black-rot-infested vineyard in New York, USA. Following two seasons of disease-conducive weather conditions, no black rot was detected on treated vines, whereas leaf and fruit infections developed on the untreated control vines. These results confirmed the efficacy of the protocol for eradicating black rot from vineyards while allowing vines to return quickly to previous yield and quality levels without replanting. The protocol may have applicability to disease eradication protocols for other perennial crops as well. Evidence is also presented on the efficacy and potential pitfalls of burning infected grapevine material to eradicate E. ampelina.