Plant diseases significantly reduce crop yields, threatening food security and agricultural sustainability. Fungi are the most destructive type of phytopathogen, and they are responsible for major yield losses in some of the most crucial crops grown across the world. In this study, a fungus isolate was detected from infected tomato plants and molecularly identified as Pythium aphanidermatum (GenBank accession number MW725032). This fungus caused damping-off disease and was shown to be pathogenic. Moreover, the expression of five pathogenesis-related genes, namely PR-1, PR-2, PR-3, PR-4, and PR-5, was quantitatively evaluated under the inoculation of tomato with P. aphanidermatum. The quantitative polymerase chain reaction (qPCR) showed that the expression levels of PR-1, PR-2, and PR-5 genes went up significantly at 5 days post-inoculation (dpi). The expression of the PR-1 gene also increased the variably, which reached its highest value at 20 dpi, with a reported relative expression level 6.34-fold higher than that of the control. At 15 dpi, PR-2 and PR-5 increased the most, while PR-1, PR-3, and PR-5 also increased noticeably at 20 dpi. On the contrary, PR-4 gene expression significantly decreased after inoculation, at all time intervals. Regarding PR-5 gene expression, the data showed a variable change in PR-5 gene expression at a different sample collection period. Still, it was highly expressed at 15 dpi and reached 3.99-fold, followed by 20 dpi, where the increasing percentage reached 3.70-fold, relative to the untreated control. The HPLC analysis indicated that the total concentration of all detected polyphenolic compounds was 3858 µg/g and 3202.2 µg/g in control and infected plant leaves, respectively. Moreover, the HPLC results concluded that Pythium infection decreased phenolic acids, such as chlorogenic and ellagic acids, which correlated with the infection–plant complex process. Based on the results, P. aphanidermatum could be a biotic stress pathogen that causes the expression of pathogen-related genes and stops the regulation of defensin phenolic compounds.