South Africa born batsman Pietersen missed practice at The Oval here Tuesday, where the third Test starts on Thursday and was placed on a course of antibiotics.
But Vaughan, speaking at The Oval on Wednesday, said: "He's alright. He's had a net. He didn't take part in the run-around and fielding drill but he'll be fine to go into tomorrow's game.
"It was just a virus," added Vaughan. "He's on antiobiotics but he seems fine. It was slightly worrying when I heard he had a virus but the doctor said straight away as long as gets his tablets down he'll be okay.
"It's a big relief for the team."
Pietersen, 27, has not missed a Test match since making his debut against Australia at Lord's two years ago and averages 52 in 29 appearances.
England must win at The Oval to square the series 1-1 and so preserve their six-year unbeaten run in home Test campaigns.
Vaughan said England would, illness permitting, field the same side that lost the second Test by seven wickets at Trent Bridge.
That would mean uncapped fast bowler Stuart Broad, again included in the squad, having to wait once more for his Test debut.