The Southampton striker, making his international bow at the ripe old age of 31, leapt highest to a corner in the 70th minute before powering a bullet header beyond Allan McGregor.
The Liverpudlian had barely been on the pitch for three minutes and the joy etched on his face was a genuinely heart-warming sight in an age when friendly internationals are often viewed as little more than a nuisance.
That Lambert's intervention signified the first time the home side had been ahead tells you all you need to know about this fixture from an English point of view.
Roy Hodgson's team yet again failed to keep a clean sheet as Scotland twice took the lead, through James Morrison and then Kenny Miller, only to be pegged back on each occasion by English equalisers from Theo Walcott and Danny Welbeck.
England, ranked 36 places above Scotland, must surely know deep down that performances like this hardly augur well for the road to the World Cup in Brazil, which is still obscured by matches against Moldova, Ukraine, Montenegro and Poland.
Though their fate is still in their own hands, England, on this evidence, are far from guaranteed to win those remaining matches.
The opening exchanges here did not hint at the flurry of goals that was to come. England dominated, aside from a Scottish punt from the back up to Miller, who could only chase forlornly.
The home side were taken by complete surprise when Scotland's goal arrived on 11 minutes. The ball fell from a corner to Morrison and the midfielder shot through a sea of players at Joe Hart's goal.
The England keeper looked to have the shot covered easily, but the ball, soaking due to the adverse weather conditions, slipped off his hands and into the back of the net. It was the softest of goals but that mere detail did not matter one iota to the Scottish fans who erupted in joy.
Morrison skidded on his knees across the sodden Wembley turf and was mobbed by his team-mates. The goal was a total embarrassment from an English perspective. Hart grimaced immediately after the ball had evaded his grasp, though the three home players who turned their backs on Morrison as he shot were hardly blameless either.
Jack Wilshere, making his eighth appearance for his country, had called on England to make Wembley a fortress before kick-off. Yet England, who lost the last time Scotland came to Wembley for a Euro 2000 play-off, were completely out of sorts.
Passes were going astray and Scotland were becoming bolder with each attack. If the visitors made a mistake, it was in becoming too committed going forward. In Walcott, England had a player with pace to burn and the Arsenal man used his engine to good effect in scoring his side's first equaliser on 29 minutes.
Tom Cleverly slid a slick pass in behind the Scotland defence. Walcott broke clear and, after cutting inside of the backtracking Steven Whittaker, finished adroitly with his left foot.
The goal enlivened the home side, whose movement had hitherto been non-existent. Now players were finally passing and moving, and there was a greater onus on one-touch plays. One such move saw Wilshere dash past two Scotland defenders before laying off to Rooney. The Manchester United forward played a one-two with Welbeck before shooting narrowly wide.
Any notion that England — who swapped Wilshere for Frank Lampard at the interval — would take control from this point on was dispelled at the beginning of the second half when Scotland's Miller scored a scorcher from the edge of the area to give the visitors the lead again.
The Vancouver Whitecaps striker fashioned some space by jinking one way, then the other — totally deceiving Gary Cahill — before driving with his left foot beyond the despairing drive of Hart.
Only a brilliant save from McGregor prevented England from equalising almost immediately when defender Russell Martin nearly flicked a Steven Gerrard free kick into his own net.
Moments later, Gerrard did provide England's second, floating a set piece to Welbeck who scored with a textbook downward header that left McGregor with no chance.
Soon afterwards, Hodgson threw on Alex Oxlade-Chamberlain for Steven Gerrard, though "The Ox" saw little of the ball as the game lost its rhythm.
Kyle Walker, Lampard and Walcott all went into the referee's book in quick succession, the former duo for cynically halting Scottish counter-attacks.
England withdrew Rooney for Lambert and the Kirkby-born forward immediately seized his chance with a thumping header that left McGregor rooted to the spot.
Lambert would strike the post in the game's dying embers as England held on for the win. Scotland, whose hopes of reaching the World Cup were extinguished long ago, perhaps deserved better.
Hodgson, for now, has much to ponder before next month's qualifier against Moldova.
His side again failed to keep a clean sheet, a familiar pattern over the past year. Only three of England's last 12 matches have seen a defensive shut-out and two of those were against San Marino.
Hart's form, too, was patchy again. He was badly at fault for Scotland's first goal and, while he can hardly be held to account for the second, genuinely world-class keepers at the top of their game may have kept out Miller's effort.
England fans will expect better when they return here on September 6.