First-pass cardiac MR perfusion (CMRP) imaging allows identification of hypo-perfused areas in the myocardium and therefore helps in early detection of coronary artery disease (CAD). However, its efficacy is often limited by respiratory motion artifacts, especially in stress-induced sequences. These distortions lead to unreliable estimates of perfusion linked parameters, such as the myocardial perfusion reserve index (MPRI). We propose a novel, robust motion correction method that suppresses motion artifacts in the frequency domain. The method is validated using rest and stress perfusion datasets of 10 patients and is compared to a state-of-the-art independent component analysis based method. Contrary to the latter, the proposed method reduces the remaining motion to less than the pixel size and allows the reliable computation of the MPRI. The strong agreement between perfusion parameters based on expert contours and after applying the proposed method enables the near-automated quantitative analyses of stress MR perfusion sequences in a clinical setting.