Instead, he played through pain and took eight wickets to bag the man-of-the-match award in the final test at Sydney.
"There's bits of bone floating around (and) we were thinking about doing it then and there and missing the rest of the series," he told reporters.
"But I wanted to play five games. I wanted to be a part of it for the whole thing."
With 22 scalps to his name, Harris emerged as the second highest wicket-taker in the Ashes for Australia behind fellow quick Mitchell Johnson.
He needs to remove fragments of floating bone from his right knee but was confident it would not hamper him from bowling against the top-ranked test team in the world.
"My knee is no different now than it was a month ago or six weeks ago," Harris added.
"Unless something really bad goes wrong, which I don't think it will, after Africa we'll get back and we've got enough time off to get it cleaned up and go from there."
Australia will play three tests in South Africa starting with the first match in Centurion from February 12.
(Writing by Sudipto Ganguly; editing by Justin Palmer)
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