Background The speed of physiological recovery from stress may be a marker for cardiovascular disease risk. Stress management programs that incorporate guided breathing have been shown to moderate the stress response and augment recovery. Objective The aim of this study was to examine the effectiveness of an app-based brief relaxation intervention (BioBase) for facilitating physiological recovery in individuals exposed to a brief psychological stressor. Methods A total of 75 participants (44 women) completed a stressor speech task and were randomly assigned to one of three conditions: control, rumination, or an app-based relaxation breathing (BioBase) conditions. Heart rate variability (HRV) was assessed as a measure of autonomic function at baseline (6 min), during stress (6 min), and during recovery (6 min). Results There was a significant increase in subjective stress following stress exposure, but the ratings returned to baseline after recovery in all three groups. In addition, there was a significant decrease in vagally mediated HRV in the poststress period. During recovery, the root mean square of successive differences (P<.001), the percentage of successive interbeat (RR) intervals that differ by >50 ms (pNN50; P<.001), and high-frequency (P<.02) HRV were significantly higher in the BioBase breathing condition than the rumination and control conditions. There was no difference in HRV values between the rumination and control conditions during recovery. Conclusions App-based relaxed breathing interventions could be effective in reducing cardiovascular disease risk. These results provide additional utility of biofeedback breathing in augmenting physiological recovery from psychological stress.