Andres Iniesta's spectacular strike deep into stoppage time wrecked Chelsea's dreams of a second successive Champions League final against Manchester United amid chaotic scenes at Stamford Bridge.
Chelsea looked to have kept Barcelona at bay and sealed an all-Premier League clash in Rome on a night of nerve-jangling tension after Michael Essien's 20-yard blockbuster in the ninth minute.
But with Guus Hiddink's side hanging on - and fuelled by a sense of injustice after referee Tom Ovrebo rejected a succession of penalty appeals - Iniesta beat Petr Cech from the edge of the area to send Barcelona into the final on away goals.
It was a heartbreaking moment for Chelsea and one that was too much to bear for Didier Drogba, on the sidelines after being substituted with an injury.
Hiddink unhappy with penalty decisions
There had already been angry scenes in the technical area after Barcelona's leveller, with Hiddink appearing to be buffeted on the touchline, but at the final whistle, Drogba marched on to the field to subject referee Ovrebo to a prolonged verbal tirade.
He rightly received a yellow card, but Drogba refused to be deterred by this punishment and continued to pursue the official while being held back.
It was an unpalatable conclusion to a dramatic encounter in which Chelsea had four appeals for penalties ignored, the strongest being a clear handball by Gerard Pique after the break.
Barcelona now face United in the final - but it was victory at a price with Dani Alves ruled out of the final after a booking and Eric Abidal also missing after he was unluckily sent off for tangling with Nicolas Anelka.
Chelsea, meanwhile, must now gather their forces for the end of the Premier League campaign and the FA Cup final against Everton.
They looked on their way to the final after a superb defensive display that restricted the visitors all night until Iniesta's deadly strike.
Barcelona's attempt to secure a crucial away goal suffered a blow before kick-off when Thierry Henry was ruled out with a knee injury - while Chelsea included both Drogba and Anelka in their line-up.
The Catalan giants posed the first threat when Xavi's effort took two deflections before Jose Bosingwa cleared from almost on the goal-line.
And Chelsea took advantage of that escape to make the breakthrough after only nine minutes.
Frank Lampard's pass was half-cleared, and even though there seemed little danger, Essien met the loose ball with a thunderous left-foot volley that left Valdes stranded as it ripped high past him and into the net off the bar.
Barcelona's response was predictably measured as they refused to stray from their trademark passing approach, but it failed to reap any rewards as Chelsea keeper Cech remained well protected by his defenders.
Indeed, it was Chelsea who had the better chances despite having less of the possession, with Valdes just beating Drogba to Lampard's long ball before diverting away the striker's angled free-kick with his knees.
Chelsea made the first of a series of penalty appeals when Malouda appeared to be hauled down by Alves inside the box, only for the referee to signal a free-kick just outside the area.
Drogba was the next to appeal when he was tugged back by Abidal, but Ovrebo ignored his claims - much to the obvious disgust of Chelsea's high-maintenance striker.
The home side, predictably, came under pressure in the opening exchanges after the break, but they broke away to great effect, only to see Drogba waste a perfect chance to double their lead.
Anelka set him up 12 yards out, but after cutting inside Pique, Drogba shot against the legs of Valdes, with Malouda striking the rebound into the side-netting.
Drogba was again left appealing in vain for a penalty after colliding with Yaya Toure, but Barcelona's giant midfield man looked to have just got a touch on the ball.
Referee Ovrebo was on the receiving end of Barcelona's anger after 65 minutes when he sent off defender Abidal after what only appeared to be an unwitting tangle of legs with Anelka.
And Ovrebo was in action again 10 minutes from time when Pique handled under pressure from Anelka, but once again the referee was in no mood to point to the spot.
Guardiola pays respects to Hiddink
As the game entered the final minutes of stoppage time, the one moment of magic Chelsea feared from this gifted Barcelona side arrived to steal their dreams of a second successive final away from them at the last gasp.
Essien sliced his clearance and the ball came to Iniesta, who sent a rising 20-yard drive past Cech into the top corner to spark chaotic scenes on the touchline.
More drama was to follow when Chelsea's players appealed one last time for a penalty when Michael Ballack's volley appeared to strike Samuel Eto'o's arm - and the German midfielder chased the referee back up the pitch to express his fury when the spot-kick never came.
And when the final whistle blew, Drogba marched on to direct his tirade at referee Ovrebo - it was an act that only increased the sense of anger and injustice on the air on a night of bitter disappointment for Chelsea.