He also took an oath later to testify truthfully at that Congressional committee hearing.
When those oaths conflict, which one takes priority?
Note that due to the nature of Wyden's question, Clapper could not simply say that he could not answer and give as the reason for not answering that it would require revealing classified information, because that itself would strongly imply that the answer was "yes".
Also, didn't Wyden already know the answer to the question? I thought I read that the members of the Senate Select Committee on Intelligence (and also those of the corresponding House committee) knew about these programs. If so, then Clapper's answer (no matter what he said) would convey no relevant information to the Committee. At common law, that would rule out any possibility of it being perjury. I don't know if there is a similar exception in the relevant perjury statutes for Congressional testimony.