Soft-tissue surgeries, such as tumor resections, are complicated by tissue deformations that can obscure the accurate location and shape of tissues. By representing tissue surfaces as point clouds and applying non-rigid point cloud registration (PCR) methods, surgeons can better understand tissue deformations before, during, and after surgery. Existing non-rigid PCR methods, such as feature-based approaches, struggle with robustness against challenges like noise, outliers, partial data, and large deformations, making accurate point correspondence difficult. Although learning-based PCR methods, particularly Transformer-based approaches, have recently shown promise due to their attention mechanisms for capturing interactions, their robustness remains limited in challenging scenarios. In this paper, we present DefTransNet, a novel end-to-end Transformer-based architecture for non-rigid PCR. DefTransNet is designed to address the key challenges of deformable registration, including large deformations, outliers, noise, and partial data, by inputting source and target point clouds and outputting displacement vector fields. The proposed method incorporates a learnable transformation matrix to enhance robustness to affine transformations, integrates global and local geometric information, and captures long-range dependencies among points using Transformers. We validate our approach on four datasets: ModelNet, SynBench, 4DMatch, and DeformedTissue, using both synthetic and real-world data to demonstrate the generalization of our proposed method. Experimental results demonstrate that DefTransNet outperforms current state-of-the-art registration networks across various challenging conditions. Our code and data are publicly available.