Ricky Lambert scored the winner and claimed: "I'll remember that all my life."
Lambert, 31, came off the bench on 62 minutes, and two minutes and 25 seconds later headed home the third and decisive goal to put a dogged Scotland to the sword at Wembley tonight.
Twice Scotland took the lead through James Morrison and Kenny Miller, but twice they were pegged back with strikes from Theo Walcott and Danny Welbeck, before the Southampton striker making his international debut spoiled the show for the thousands of travelling Tartan Army supporters.
It was an pulsating game, played with pace and grit, befitting those two rivals.
England rued their chance to take command as the visitors took the lead on 11 minutes in sensational style.
A corner was half cleared by Danny Welbeck. Up popped James Morrison just outside the England penalty area and he rifled a powerful right-footer on target.
Joe Hart inexplicably allowed the ball to bounce off his body and the ball ended up in the back of the net.
England regained control of the match thorough excellent possession, which resulted, on 18 minutes with Theo Walcott shooting from distance, but high over Allan McGregor's goal.
A swift break by England on 26 minutes saw Walcott flash a right wing ball across goal. Rooney should have left it but got his foot to it. fortunately the ball fell to Tom Cleverley, but the Manchester United midfielder failed to capitalise.
But the home side finally pierced a stubborn Scottish defence two minutes later.
A fine defence-splitting ball by Cleverley, found Walcott racing clear on the right.
The Arsenal wide man raced into the Scottish penalty area, cut the ball back past Steven Whittaker, and in one swift movement lashed the ball low with his left foot past a frustrated McGregor.
It was Walcott's fifth goal for England.
Rooney almost put England ahead on 33 minutes but his right-footer, after a neat set-up by Welbeck on the edge of the Scottish area, crept just wide of the goalkeeper's right post.
Two minutes from the break and Rooney had a legitimate goal chalked off for offside. Replays clearly showed that the Manchester United rebel was onside from Steven Gerrard's perfectly-placed chipped through ball.
Wilshere lasted just 45 minutes as he was replaced by Chelsea midfield maestro Frank Lampard at half-time.
But it was Scotland who retook the lead three minutes after the restart.
With the England fence with their hands up for a non-existent offside Kenny Miller reacted quickest, twisting the blood of a prone Gary Cahill to power a curling left-footer past the disparing dive of Hart from the edge of the area.
But England were not unbowed and on 52 minutes they struck back.
A classic right-footed free-kick by Gerrard fell invitingly to Welbeck and the striker headed past McGregor to level the score.
Kyle Walker received the first yellow card of the feisty encounter when he upended James Forrest on 56 minutes.
Walcott swiftly became numb two along with Robert Snodgrass as tempers flared.
Lampard forced McGregor into a fine save on 60 minutes.
Alex Oxlade-Chamberlain entered the fray on 62 minutes, replacing Gerrard.
Lampard, now, skipper, became the third England player to get a yellow card for scything down Russell Martin a minute later.
A swathe of subsitutions then took place, the most important being Ricky Lambert, who within three minutes of coming on for Rooney, powerfully headed home from a Baines corner from eight yards out to put England into the lead.
The 31-year-old Southampton striker will always remember his touch touch as an England player.
Lampard almost made it number four with 13 minutes to go, but his trademark blaster from 39-yards, was magnificently tipped over the crossbar by McGregor.
Substitute Wilfred Zaha then had a chance, but went for goal instead of passing, and the ball zipped across goal and away to safety.
With the seconds ticking down Scotland went in search for the equaliser and on a swift break conjured up by Steven Naismith and Whitaker on the left, saw the left back Whittaker arrow a fine left-footer just over Hart's crossbar from an acute angle.
But it was England who almost got the fourth deep into added time.
A fine breakaway saw England pass their way through a dishevelled and Zaha set -up Lambert to slot home, but the striker could only smack the ball onto the Scottish left upright with the goal gaping.
That was the last of the action.
Teams: Hart, Walker, Baines, Gerrard, Cahill, Jagielka, Walcott, Wilshere, Welbeck, Rooney,Cleverley,
Subs: Johnson, Foster, Cole, Jones, Smalling, Milner, Lampard, Defoe, Lambert, Oxlade-Chamberlain, Zaha, Ruddy
Scotland: McGregor, Hutton, Whittaker, Martin, Hanley, Maloney, Morrison, Brown, Miller, Snodgrass, Forrest.
Subs: Gilks, McArthur, Naismith, Burke, Adam, Webster, Rhodes, Mulgrew, Bannan, Marshall, Griffiths, Mackay-Steven, Dorrans, Conway, Boyd, Greer, Hammell
Referee Felix Brych (Germany)
