Flooding is an abiotic stress that creates hypoxic conditions triggered by redox potential leading to restricted growth and grain yield in plants. In the current study, we have investigated the effect of exogenous gibberellins (GA4+7) on soybean under flooding stress. A regulatory role of GAs on biochemical changes in soybean plants [including chlorophyll contents, endogenous bioactive GA1 and GA4, endogenous jasmonic acid (JA) and abscisic acid (ABA)] has been elucidated after 3 and 6 h of flooding stress. The modulation of stress-related bio-chemicals and their genetic determinants [for instance, ABA (Timing of CAB expression1—TOC1, ABA-receptor—ABAR) and NO (S-nitrosoglutathione reductase—GSNOR1, NO overproducer1—NOX, and nitrite reductase—NR)] in response to short-term flooding stress were also explored. The current study showed that exogenous GAs rescued chlorophyll contents, enhanced endogenous bioactive GA1 and GA4 levels, endogenous jasmonic acid (JA) and checked the rate of ABA biosynthesis under short-term flooding. The exo-GAs induced the glutathione activity and reduced the resulting superoxide anion contents during short-term flooding in Pungsannamul soybean. Exo-GAs also triggered the endogenous S-nitrosothiols (precursor for increased NO production) that have been decreased over the time. Moreover, the exo-GAs could impinge a variety of biochemical and transcriptional programs that are ameliorative to plant growth during short-term flooding stress. The presence of GA1 and GA4 also confirms the presence of both C13-hydroxylation pathway and non-C13-hydroxylation pathway in soybean, respectively.