This study investigated the effect of prolonged exertion on cardiac parasympathetic (cPS) reorganization and associated aerobic performance in response to repeated short-lasting submaximal exercise bouts (SSE) performed for 7 days following prolonged exertion. In 19 recreational runners, heart rate (HR) and HR variability (HRV) indices (lnRMSSD, lnHF, and lnLF/HF) were monitored pre- and post-submaximal graded cycling performed on consecutive days following a half-marathon (HM) and compared with the baseline, pre-HM values. Additionally, HR recovery (HRR), aerobic performance, and rate of perceived exertion (RPE) were determined. HR, HRV indices, and HRR were tested for correlation with exercise performance. A significant time effect was found in HR, HRR, and HRV indices as well as in aerobic performance and RPE during the study period. Most of the measured parameters differed from their baseline values only on the same day following HM. However, HRR and HR measured in recovery after SSE were additionally affected one day following the half-marathon yet in opposite directions to those recorded on the same day as the HM. Thus, postSSE HR and HRR exhibited a bivariate time response (postSSE HR: 102 ± 14 bpm; p < 0.001; 82 ± 11 bpm; p = 0.007 vs. 88 ± 11 bpm; HRR in 30 s after SSE cessation: 14.9 ± 4.9 bpm; p < 0.001; 30.1 ± 13.3 bpm; p = 0.006 vs. 24.4 ± 10.8 bpm), potentially indicating a cPS dysfunction phase on the same day and cPS rebound phase one day following HM reflected also in consecutive changes in aerobic power. Correlations were found between the changes in measured cardiac indices with respect to baseline and the changes in aerobic performance indices throughout the study period. The effect of exercise history on cPS reorganization is more pronounced in response to SSE than at rest. Accordingly, we conclude that SSE performed repeatedly on a daily basis following prolonged exertion offers a noninvasive tool to evaluate the impact of training history on cPS recovery and associated aerobic power output in recreational athletes.