He didn't say that at all. He said that if they had confidence the president hadn't committed a crime, they would have said so. He further said that since DoJ policy does not allow for a sitting president to be charged, they never made a consideration into doing so. That doesn't come close to him saying that he could not prove the president is guilty.
Since when is it the responsibility of a prosecutor to prove that someone did not commit a crime? The only role of a prosecutor is to prove, through evidence, that someone did commit a crime. Presumption of innocence covers all other persons.