Dan Johnson has been giving evidence at the High Court where Sir Cliff is seeking damages from the BBC for how it reported the police investigation into alleged abuse.
The singer denied the allegations and was later cleared of any wrongdoing.
Mr Johnson was asked what he meant in an internal BBC email when he made remarks about a clip of Evangelist preacher Billy Graham rally at Bramall Lane in the 1980s, where the alleged sex assault was said to have happened.
Justin Rushbrooke QC, for Sir Cliff, said the phrases "it wasn't just the hand of God doing the touching" and "guilty in my book" were an indication of the reporter's "mindset" about the story.
The barrister said Mr Johnson was treating the singer "as a guilty man".
But Mr Johnson repeatedly denied he was referring to Sir Cliff in the email, and said the comments were about Mr Graham.
He described the "hand of God" reference as a "bad taste joke", adding: "These are light-hearted remarks made to a close colleague, it doesn't mean anything.
"It doesn't affect the way I reported this story later on."
Sir Cliff sat open-mouthed and shook his head in disbelief as Mr Johnson gave his responses to the court.
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