"England should treat the whole ball-tampering incident as a warning," he wrote in a column in the Daily Telegraph on Thursday.
"They were lucky to get away without an official reprimand, or even a ban, because there is no doubt in my mind that they were trying to change the condition of the ball."
South Africa raised concerns about the ball during the third day of the third test in Cape Town after television pictures showed England bowler Stuart Broad stopping the ball with his foot.
Footage also suggested seamer Jimmy Anderson may have been picking the seam with his thumbnail.
The International Cricket Council (ICC) decided no action would be taken, however, after South Africa made no official complaint.
Vaughan said Broad had been stopping the ball with his boot all the way through the series and recalled similar examples from his own England days.
"When I was captain, I would get my attack to bowl cross-seam bouncers at some point around the 15th over.
"You never knew which side of the ball was going to hit the pitch and become scuffed up, but after you had done it three or four times, you chose one side to shine and one to keep rough.
"Marcus Trescothick used to be our shiner: he would suck jelly babies to make one side of the ball sugary," he added.
"I don't really know whether it made any difference, but I do know that we had a good summer with reverse swing in 2005."
Vaughan and Nasser Hussain, also a former England captain, said there would have been uproar had other nationalities been involved.
"There is no doubt in my mind that, if a Pakistani or Indian bowler had been caught doing what Anderson did, we would have said he was cheating," Hussain wrote in the Daily Mail.
"I do not think the International Cricket Council have covered themselves in glory here," he added.
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