Pietersen has been axed for the final Test against South Africa after he allegedly sent controversial text messages to Proteas players criticising captain Andrew Strauss.
The ECB opted to drop Pietersen for the Test at Lord’s, despite a statement from South Africa on Monday claiming the batsman’s texts were merely “banter”.
“If it’s true that he sent those texts, it will take a long time for him to be allowed back,” former England captain Vaughan told BBC Sport.
“Strauss is as popular a captain as England have ever had.”
Pietersen called time on his international limited-overs career in May, before hinting at a possible retirement from international Test cricket following the second Test at Headingley.
But in a surprise move on Saturday, the 32-year-old committed to playing all forms of cricket for England in a YouTube interview.
Vaughan, who captained his country to Ashes success in 2005, believes the right decision has been made by the ECB, but the 37-year-old is hoping to see Pietersen make a return to the England set-up in the future.
“It’s been a mad, but also a very sad week for the England cricket team. There are no real winners, but one very big loser and that’s Kevin Pietersen,” added Vaughan.
“I don’t think he’s getting the right advice. I don’t know who is advising him but in my eyes they are not doing the right job for Kevin.
“We don’t know what has been going on behind the scenes for the last few months, because the text messages could only be a tipping point.
“There’s no way he could have arrived in that dressing room at Lord’s on Tuesday morning. It will take time, but he will get another chance. I hope he does.”
The ECB’s decision means England will be expected to field Jonny Bairstow and James Taylor against South Africa’s bowling attack at Lord’s – the pair have yet to score a half century between them in international Tests – as the hosts look to level the series.
MORE: The latest football news
MORE: The latest tennis news
BIOGRAPHY: Daniel Sturridge
BIOGRAPHY: Kepa Arrizabalaga