The influence of perceived unfairness at the workplace (organizational injustice) on employee health is well established. Several theories explain the unpleasant and stressful nature of the experience of injustice, using trust as a central element. This study examines the effect of trust to supervisor on the association of perceived injustice with vagal tone-an objective marker for stress experience. Questionnaires assessed organizational justice and trust. Vagal tone was measured by indictors of heart rate variability (HRV), which captured parasympathetic (pNN50, RMSSD, and HF) and parasympathetic and sympathetic (SDNN, and LF) regulation. Synergistic effects were tested by linear regressions with interaction terms between organizational justice and trust to supervisor in 38 managers. Organizational justice was related to HRV indicators that reflect in particular the parasympathetic branch (beta(pNN50) = 0.32, p < 0.05; beta(RMSSD) = 0.27, p < 0.1), and interaction effects with trust to supervisor were also most pronounced there (interaction beta(pNN50) = -0.41, p < 0.01; beta(RMSSD) = -0.47, p < 0.01). In conclusion, the combination of low perceived justice and trust to supervisor appears substantial to the physiological stress threat of employees. Promoting fairness at the workplace might reduce stress; if not possible, trust to supervisor should be enhanced.