Vaughan had set his heart on making his first Test appearance since December 2005 at Lord's on Thursday after finally overcoming a string of injuries, mainly to his knee.
A broken middle finger on his right hand put paid to that, although Vaughan admits he was sorely tempted to declare himself ready to play.
"My heart was saying 'just go out and play' - but my head overruled the heart," the 32-year-old said. "I knew I could probably just about get through a game. But I might have struggled a bit in the field.
"I just thought it might be too big a risk. I was told if I get one more hit on it I could be out for two months."
In the meantime, Vaughan will be part of Team England at Lord's and he makes no apologies for his intended presence, while his stand-in Andrew Strauss is directing affairs on the field.
Vaughan wants to establish a successful working relationship with new coach Peter Moores, himself preparing for his first Test after replacing Duncan Fletcher.
"I'm going to be around this week," he said. "I know it's a magnificent talking point for many - but I am the England cricket captain, looking like missing just one game.
"Andrew will take the team out and make the decisions on the pitch, but I have to have a huge say in and around the team because of the fact it's a new regime.
"Peter and I are working together for the first time - and a week later I hope I'll be back as England captain."
All-rounder Andrew Flintoff meanwhile is facing a battle to be fit for the first Test following a recurrence of the ankle problems which have dogged his career.
Flintoff felt discomfort in his left ankle, which has been operated on twice in the last three years, while bowling nine overs for Lancashire against Hampshire over the weekend and has been forced to have a scan, the result of which will determine if he is able to play a full part at Lord's.
"We'll probably know more after I've run around and done what I need to do at practice, but I'm hopeful for Thursday," Flintoff said.
"Sometimes when it's the ankle the alarm bells start ringing a little bit, but I'm still hopeful.
"The operation was on the back and on the inside and this is more on the outside. I had a bit of discomfort in the same sort of area in the winter so it's not something completely new.
"I had a couple of twinges in Australia. It's something we have been aware of and something that has niggled away but it did get a bit worse last Friday. I struggled to play through it on Friday and we'll have to wait and see how it settles down, but fingers crossed it will be all right."
Flintoff's status as one of the world's best all-rounders has come under scrutiny of late. He scored only two half-centuries during the Ashes tour of Australia and has passed 50 only once in his last 28 one-day international innings for England.
It is one of the reasons why the selectors chose Strauss to lead the side this week in the absence of Vaughan, although Flintoff stressed: "The captaincy wasn't something I was really thinking about.
"Since I've got back from the West Indies I've been concentrating on getting my game in order and I've had a fantastic opportunity at Lancashire to do that.
"I came back a week last Sunday and from Tuesday I've been back at Old Trafford batting and bowling, managed to have a couple of games and rediscovered my form a little bit.
"The captaincy is something I'd have done if I'd have been asked, but it was not something I was hanging out for."
If Flintoff is unable to bowl at full tilt, England could opt to drop him and pick Owais Shah as a specialist batsman instead.