The authentication of grape variety from which wine is produced is necessary for protecting a consumer from adulteration and false labelling. The aim of this study was to analyze phenolic compounds in red monovarietal wines produced from Zweigelt (Vitis vinifera) and Rondo (non-Vitis vinifera) varieties while using the UPLC-PDA-MS/MS method and to assess whether these wines can be classified according to grape variety that is based on chemometric analysis. Fifty-five phenolic compounds belonging to five classes—anthocyanins, flavonols, flavan-3-ols, phenolic acids, and stilbenes—were identified and quantified in Zweigelt and Rondo wines. The wines of the Zweigelt variety were characterized by lower concentrations of phenolic compounds than those of the Rondo variety. Furthermore, wines of the Zweigelt variety contained the highest concentrations of flavan-3-ols, and wines of the Rondo variety—the highest concentrations of anthocyanins. Hierarchical cluster analysis (HCA) revealed that Zweigelt wines and Rondo wines formed two separate groups. The Rondo group was divided into two subgroups, differing in type of malolactic fermentation (spontaneous or induced). Phenolic compounds analysis by means of UPLC-PDA-MS/MS combined with HCA is a useful tool for the classification of red wines that were produced from Zweigelt and Rondo grape varieties, regardless of yeast strain and type of malolactic fermentation