Sunflower oil (Helianthus annuus) contains a rich concentration of polyunsaturated fatty acids, which are susceptible to rapid oxidative processes. The aim of this study was to evaluate the stabilizing effect of lipophilic extracts from two types of berries, sea buckthorn and rose hips, on sunflower oil. This research included the analysis of sunflower oil oxidation products and mechanisms, including the determination of chemical changes occurring in the lipid oxidation process via LC-MS/MS using electrospray ionization in negative and positive mode. Pentanal, hexanal, heptanal, octanal, and nonanal were identified as key compounds formed during oxidation. The individual profiles of the carotenoids from sea buckthorn berries were determined using RP-HPLC. The influence of the carotenoid extraction parameters ascertained from the berries on the oxidative stability of sunflower oil was analyzed. The dynamics of the accumulation of the primary and secondary products of lipid oxidation and the variation of the carotenoid pigment content in the lipophilic extracts of sea buckthorn and rose hips during storage demonstrated good stability at 4 °C in the absence of light for 12 months. The experimental results were applied to mathematical modeling using fuzzy sets and mutual information analysis, which allowed for the prediction of the oxidation of sunflower oil.