This paper describes a spoken question answering system that utilizes the uncertainty in automatic speech recognition (ASR) to mitigate the effect of ASR errors on question answering. Spoken question answering is typically performed by transcribing spoken content with an ASR system and then applying text-based question answering methods to the ASR transcriptions. Question answering on spoken documents is more challenging than question answering on text documents since ASR transcriptions can be erroneous and this degrades the system performance. In this paper, we propose integrating confusion networks with word confidence scores into an end-to-end neural network-based question answering system that works on ASR transcriptions. Integration is performed by generating uncertainty-aware embedding representations from confusion networks. The proposed approach improves F1 score in a question answering task developed for spoken lectures by providing tighter integration of ASR and question answering.