There is a growing body of research on yoga as a therapeutic intervention for psychological symptoms of post-traumatic stress disorder (PTSD) accompanied by speculations on underlying physiologic mechanisms. The purpose of this systematic review is to identify, qualitatively evaluate, and synthesize studies of yoga as an intervention for PTSD that measured physiologic outcomes in order to gain insights into potential mechanisms. The focus is on studies evaluating yoga as a therapeutic intervention for PTSD rather than for trauma exposure, PTSD prevention, or subclinical PTSD. Multiple databases were searched for publications from the past two decades using terms derived from the question, “In people with PTSD, what is the effect of yoga on objective outcomes?” Eligibility criteria included yoga-only modalities tested as an intervention for formally diagnosed PTSD with at least one physiologic outcome. Results of this review confirmed that, though much of the published literature proposes physiological mechanisms underlying yoga’s effects on PTSD, very few studies (n = 3) have actually evaluated physiological evidence. Additionally, several studies had methodological limitations. In light of the limited data supporting yoga’s beneficial effects on autonomic nervous system dysregulation, we present a theoretical model of the psychoneuroimmunologic processes associated with PTSD and the effects yoga may have on these processes to guide future research. Gaps in the literature remain for mechanisms related to activation of the hypothalamic–pituitary–adrenal axis and inflammation. Additional rigorous mechanistic studies are needed to guide development of effective yoga interventions for PTSD to augment existing evidence-based PTSD treatments.