Ecological food preservation and freshness prolongation is an important issue in the food industry. Most of the common methods required the addition of chemical preservatives which is widely criticized. In this article, a novel approach for herbs keeping by ozonation is presented. The process is studied both in experimental and modeling approaches. The considered parameters were dry mass, l-ascorbic acid concentration, carotenoids, essential oils, flavonoids, and polyphenols content. Also, the antioxidation activity of tested food is verified. The experiment examined the impact of ozonation with concentration up to 0.9 ppm, on the 7-days storage of mint and rosemary in refrigerated conditions. The positive impact of ozone on almost all the tested parameters was proved for moderate concentrations of this factor. The one exception was essential oils, which turned out to be too susceptible for oxidation. The presented mathematical model indicated very good convergence with experimental results—the mean relative error, except essential oil, does not exceed 2% for both of the tested herbs. This indicated clearly that the presented tool can be used for further optimization of the process, with high practical application.