The emergence of robotics could enable ophthalmic microsurgical procedures that were previously not feasible due to the precision limits of manual delivery, for example, targeted subretinal injection. Determining the distance between the needle tip, the internal limiting membrane (ILM), and the retinal pigment epithelium (RPE) both precisely and reproducibly is required for safe and successful robotic retinal interventions. Recent advances in intraoperative optical coherence tomography (iOCT) have opened the path for 4D image-guided surgery by providing near video-rate imaging with micron-level resolution to visualize retinal structures, surgical instruments, and tool-tissue interactions. In this work, we present a novel pipeline to precisely estimate the distance between the injection needle and the surface boundaries of two retinal layers, the ILM and the RPE, from iOCT volumes. To achieve high computational efficiency, we reduce the analysis to the relevant area around the needle tip. We employ a convolutional neural network (CNN) to segment the tool surface, as well as the retinal layer boundaries from selected iOCT B-scans within this tip area. This results in the generation and processing of 3D surface point clouds for the tool, ILM and RPE from the B-scan segmentation maps, which in turn allows the estimation of the minimum distance between the resulting tool and layer point clouds. The proposed method is evaluated on iOCT volumes from ex-vivo porcine eyes and achieves an average error of 9.24 µm and 8.61 µm measuring the distance from the needle tip to the ILM and the RPE, respectively. The results demonstrate that this approach is robust to the high levels of noise present in iOCT B-scans and is suitable for the interventional use case by providing distance feedback at an average update rate of 15.66 Hz.