Ozonated water is being introduced as an alternative phytosanitary treatment to control grapevine diseases in a context in which the reduction of chemical pesticides has become an urgent necessity. In this study, we evaluated the effect of spraying grapevines with ozonated water on the enological, phenolic, and aromatic qualities of Bobal wines during two consecutive growing seasons. In the first season, ozonated water was applied once during the ripening period on grapevines trained on the traditional gobelet system (S1). In the second season, three applications were performed between fruit set and harvest on grapevines grown on a vertical trellis system (S2). The S1 treatment led to a wine with an increased alcoholic degree and a remarkably higher phenolic content, which resulted in preferable chromatic characteristics. The S2 treatment maintained the total phenolic content but significantly enhanced stilbenes and flavanols and also reduced anthocyanins, which negatively affected the wine colour. Regarding aroma, both treatments reduced the content of glycosylated precursors and had different effects on free volatiles, both varietal and fermentative. Thus, the metabolic response of grapevines to the ozonated water stress, and therefore the quality of wines, depended on the ozone dose received by the plants.