We consider the problem of vision-based pose estimation for autonomous systems. While deep neural networks have been successfully used for vision-based tasks, they inherently lack provable guarantees on the correctness of their output, which is crucial for safety-critical applications. We present a framework for designing certifiable neural networks (NNs) for perception-based pose estimation that integrates physics-driven modeling with learning-based estimation. The proposed framework begins by leveraging the known geometry of planar objects commonly found in the environment, such as traffic signs and runway markings, referred to as target objects. At its core, it introduces a geometric generative model (GGM), a neural-network-like model whose parameters are derived from the image formation process of a target object observed by a camera. Once designed, the GGM can be used to train NN-based pose estimators with certified guarantees in terms of their estimation errors. We first demonstrate this framework in uncluttered environments, where the target object is the only object present in the camera's field of view. We extend this using ideas from NN reachability analysis to design certified object NN that can detect the presence of the target object in cluttered environments. Subsequently, the framework consolidates the certified object detector with the certified pose estimator to design a multi-stage perception pipeline that generalizes the proposed approach to cluttered environments, while maintaining its certified guarantees. We evaluate the proposed framework using both synthetic and real images of various planar objects commonly encountered by autonomous vehicles. Using images captured by an event-based camera, we show that the trained encoder can effectively estimate the pose of a traffic sign in accordance with the certified bound provided by the framework.