Sample-wise detection of P-, R-, and T-peaks in electrocardiograms (ECGs) is challenging because each peak type is sparsely represented (≈1:500 samples in a typical 10-s, 500-Hz ECG at 60 bpm), such that even a small number of false-positives (FPs) can markedly degrade positive predictive value (PPV) and limit the practicality of classifier-only approaches. This study proposes a lightweight ECG peak detection framework that combines binary classifiers with a physiological temporal constraints (PTC) algorithm to address extreme sample-level class imbalance. Local morphological features are first evaluated using lightweight machine-learning models, among which XGBoost (XGB) exhibited the most stable score-ranking performance. Rather than directly thresholding classifier outputs, prediction scores are interpreted through PTCs that encode physiological timing relationships. R-peaks are detected using score ranking combined with a refractory-period constraint, and the detected R-peaks serve as temporal landmarks for subsequent P- and T-peak detection within physiologically plausible time windows reflecting the P–QRS–T sequence. Quantitative evaluation was conducted using the Lobachevsky University Electrocardiography Database, hereafter referred to as LUDB. With a temporal tolerance of ±20 ms, the XGB-based system achieved an F1-score of 0.87 for R-peak detection (sensitivity 0.96, PPV 0.79), corresponding to approximately 9–10 true R-peaks with only 2–3 FP samples per 10-s segment. For P- and T-peaks, F1-scores of 0.70 and 0.69 were obtained, respectively. Additional evaluation on arrhythmic LUDB records and qualitative application to ECG recordings from the PTB-XL database demonstrated physiologically consistent behavior. These results indicate that reliable and interpretable ECG peak detection under extreme class imbalance can be achieved by integrating lightweight classifiers with explicit PTC algorithms, without reliance on complex deep learning architectures.