Respiratory rate and heart rate variability (HRV) are studied as stress markers in a database of young healthy volunteers subjected to acute emotional stress, induced by a modification of the Trier Social Stress Test. First, instantaneous frequency domain HRV parameters are computed using time-frequency analysis in the classical bands. Then, the respiratory rate is estimated and this information is included in HRV analysis in two ways: 1) redefining the high-frequency (HF) band to be centered at respiratory frequency; 2) excluding from the analysis those instants where respiratory frequency falls within the low-frequency (LF) band. Classical frequency domain HRV indices scarcely show statistical differences during stress. However, when including respiratory frequency information in HRV analysis, the normalized LF power as well as the LF/HF ratio significantly increase during stress ( p-value 0.05 according to the Wilcoxon test), revealing higher sympathetic dominance. The LF power increases during stress, only being significantly different in a stress anticipation stage, while the HF power decreases during stress, only being significantly different during the stress task demanding attention. Our results support that joint analysis of respiration and HRV obtains a more reliable characterization of autonomic nervous response to stress. In addition, the respiratory rate is observed to be higher and less stable during stress than during relax ( p-value 0.05 according to the Wilcoxon test) being the most discriminative index for stress stratification (AUC = 88.2 % ).