Scott said he could not afford to chase a further appeal in the Supreme Court, but maintained his innocence.
"I'm 73 tomorrow, and I would never do such a thing."
He said he had worked as a teacher all his life and never had a complaint about his conduct.
One of the points of Scott's appeal revolved around his penis being measured in court.
During the trial last year, Scott's penis was measured by a doctor with a wooden ruler to determine if it was the same length as what the victim felt pressing into her, as there had been an argument it could have been a wallet she felt.
The measurement was suppressed.
Scott's lawyer Barbara Hunt told the appeal court measuring her client's penis was a trial tactic that misfired.
The measuring tactic was like a "schoolboy's locker room joke that went wrong", Hunt said, adding it would have been shocking and unsettling for the jury.
"It was degrading to the appellant, it was insulting to the complainant, it attracted a frenzy of attention."
Hunt argued the measurement was an error that risked a miscarriage of justice.
"If it hadn't happened that way, it could well have been a different outcome."
Hunt also pointed to additional medical evidence which should have been called at trial, the details of which are suppressed.
But the Court of Appeal judges were not satisfied the new evidence would have made a difference to the outcome of the trial.
They also said in their judgment the measuring of the penis was a "legitimate trial strategy".
In his appeal, Scott sought to have his conviction overturned and failing that, he challenged the decision not to allow him a discharge without conviction.
Both strands of his appeal failed.
Council chief executive Wayne Maxwell said Scott would be removed from office immediately.
"He cannot carry out any further duties as a councillor," he said.
"Any councillor convicted of a crime that carries a maximum penalty of two years or more imprisonment is disqualified from office. This applies to the charge Councillor David Scott has been convicted of."