Heart rate variability (HRV) reflects dynamic variation in sympathetic and parasympathetic nervous system (SNS and PNS) activity. The parasympathetic vagus nerve is responsible for HRV between 0.12 and 0.4 Hz, which is thought to index the capacity for effective coping, and is linked to physical and emotional well-being. Yogic breathing to increase vagal activity is often paced below 0.12 Hz (< 7.2 breaths per minute (BrPM)), where its impact HRV can be due to both sympathetic and parasympathetic mechanisms. Five healthy volunteers completed three pharmacological blockade sessions (placebo, sympathetic blockade with Esmolol, and parasympathetic blockade with Glycopyrrolate) about 48 hours apart, and during each session completed 11 Sudarshan Kriya Yogic breathing exercises at 4-9 BrPM. HRV was the lowest under Glycopyrrolate (p < 0.001), and there was no significant difference between placebo and sympathetic blockade with Esmolol. In addition, the spectral power of specific HRV frequencies was greatest at similar frequencies of breathing, a pattern prevented only by Glycopyrrolate. These findings suggest that heart rate is vagally influenced at all breathing rates, and that the SNS is not the mechanism by which slow breathing increases HRV.