In addition, Skelton was shown a yellow card for foul play in a decision which looked certain to kill Australia's momentum, their chance at pulling off a victory and ultimately any chance they had at becoming the first Australian team since 1984 to complete the grand slam.
Skelton's blushes were saved by a superb individual try to Tevita Kuridrani four minutes from time which sealed a stunning 23-22 victory - but they weren't enough to appease Cheika, who had no objections to the sin-binning.
"(Skelton has) got to put his arms around that guy and he knows that. It's ill- disciplined from him," Cheika said.
"Those decisions come down to the ref - whether it's a penalty or a yellow, but regardless it's an offence.
"He doesn't have to do it. We had our own penalty, it's after the whistle and it wasn't clever.
"He knows that himself. I don't even need to tell him so I don't think he'll be worried about me saying it here."
Skelton returned to the field with one minute left in regular time and was part of the gritty Wallabies defence which repelled phase after phase of Scottish attacks in the famous victory.
- AAP