Diseases and climate change are major factors limiting grape productivity and fruit marketability. Lasiodiplodia theobromae is a fungus of the family Botryosphaeriaceae that causes Botryosphaeria dieback of grapevine worldwide. Abiotic stress may change host vitality and impact susceptibility to the pathogen and/or change the pathogen’s life cycle. However, the interaction between both stress drivers is poorly understood for woody plants. We addressed the hypothesis that distinct morpho-physiological and biochemical responses are induced in grapevine (Vitis vinifera)–L. theobromae interactions depending on when water deficits are imposed. Grapevines were submitted to water deficit either before or after fungus inoculation. Water deficit led to the reduction of the net photosynthetic rate, stomatal conductance, and transpiration rate, and increased the abscisic acid concentration regardless of fungal inoculation. L. theobromae inoculation before water deficit reduced plant survival by 50% and resulted in the accumulation of jasmonic acid and reductions in malondialdehyde levels. Conversely, grapevines inoculated after water deficit showed an increase in proline and malondialdehyde content and all plants survived. Overall, grapevines responded differently to the primary stress encountered, with consequences in their physiological responses. This study reinforces the importance of exploring the complex water deficit timing × disease interaction and the underlying physiological responses involved in grapevine performance.