Autonomic dysfunction is an independent predictor of cardiovascular and all-cause mortality after myocardial infarction (MI). We tested the effects of a 12-week yoga-based cardiac rehabilitation program on heart rate variability (HRV) in 80 patients post-MI. This randomized controlled trial with two parallel groups was carried out in a tertiary care institution in India. The yoga group received 13 hospital-based structured yoga sessions as an adjunct to standard care. Control group participants received enhanced standard care involving three brief educational sessions with a leaflet on the importance of diet and physical activity. HRV was measured in all participants with lead II electrocardiogram (ECG) signals. One yoga group patient's data were excluded due to ECG abnormalities. Baseline measurement was done 3 weeks post-MI, and postintervention assessment took place at the 13th week. HRV frequency and time domain indices were analyzed. There were no significant between-group differences in the HRV time domain indices. Frequency domain indices showed significant between-group differences in HF power (absolute) (yoga vs. control: 114.42 [−794.80–7,993.78] vs. −38.14 [−4,843.50–1,617.87], p = 0.005) and total power (nu) (yoga vs. control: 44.96 [21.94] vs. −19.55 [15.42], p = 0.01) with higher HF power and total power (nu) in the yoga group. It should be noted that these results cannot be generalized to high risk patients. Respiratory frequency control to check for influence of respiratory rate on RR interval was not evaluated. This short-term yoga-based cardiac rehabilitation program had additive effects in shifting sympathovagal balance toward parasympathetic predominance while increasing overall HRV in optimally medicated post-MI patients.