Dense 3D facial motion capture from only monocular in-the-wild pairs of RGB images is a highly challenging problem with numerous applications, ranging from facial expression recognition to facial reenactment. In this work, we propose DeepFaceFlow, a robust, fast, and highly-accurate framework for the dense estimation of 3D non-rigid facial flow between pairs of monocular images. Our DeepFaceFlow framework was trained and tested on two very large-scale facial video datasets, one of them of our own collection and annotation, with the aid of occlusion-aware and 3D-based loss function. We conduct comprehensive experiments probing different aspects of our approach and demonstrating its improved performance against state-of-the-art flow and 3D reconstruction methods. Furthermore, we incorporate our framework in a full-head state-of-the-art facial video synthesis method and demonstrate the ability of our method in better representing and capturing the facial dynamics, resulting in a highly-realistic facial video synthesis. Given registered pairs of images, our framework generates 3D flow maps at ~60 fps.