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E3 ubiquitin ligases play important roles in plant immunity, but their role in soybean has not been investigated previously. Here, we used <i>Bean pod mottle virus</i> (BPMV)-mediated virus-induced gene silencing (VIGS) to investigate the function of <i>Gm</i>SAUL1 (Senescence-Associated E3 Ubiquitin Ligase 1) homologs in soybean. When two closely related <i>SAUL1</i> homologs were silenced simultaneously, the soybean plants displayed autoimmune phenotypes, which were significantly alleviated by high temperature, suggesting that <i>Gm</i>SAUL1a/1b might be guarded by an R protein. Interestingly, silencing <i>GmSAUL1a/1b</i> resulted in the decreased activation of <i>Gm</i>MPK6, but increased activation of <i>Gm</i>MPK3 in response to flg22, suggesting that the activation of <i>Gm</i>MPK3 is most likely responsible for the activated immunity observed in the <i>Gm</i>SAUL1a/1b-silenced plants. Furthermore, we provided evidence that <i>Gm</i>SAUL1a is a bona fide E3 ligase. Collectively, our results indicated that <i>Gm</i>SAUL1 plays a negative role in regulating cell death and immunity in soybean.