Individuals diagnosed with systemic arterial hypertension (SAH) are considered risk groups for COVID-19 severity. This study assessed differences in cardiac autonomic function (CAF) and functional capacity (FC) in SAH individuals without COVID-19 infection compared to SAH individuals post-COVID-19. Participants comprised 40 SAH individuals aged 31 to 80 years old, grouped as SAH with COVID-19 (G1; n = 21) and SAH without COVID-19 (G2; n = 19). CAF was assessed via heart rate variability (HRV), measuring R–R intervals during a 10-min supine period. Four HRV indices were analyzed through symbolic analysis: 0V%, 1V%, 2LV%, and 2UV%. FC assessment was performed by a 6-min walk test (6MWT). G1 and G2 showed no significant differences in terms of age, anthropometric parameters, clinical presentation, and medication use. G2 exhibited superior 6MWT performance, covering more distance (522 ± 78 vs. 465 ± 59 m, p < 0.05). Specifically, G2 demonstrated a moderate positive correlation between 6MWT and the 2LV% index (r = 0.58; p < 0.05). Shorter walking distances were observed during 6MWT in SAH individuals post-COVID-19. However, the study did not find impaired cardiac autonomic function in SAH individuals post-COVID-19 compared to those without. This suggests that while COVID-19 impacted FC, CAF remained relatively stable in this population.