The Blues looked to be cruising after Michael Essien's stunning early volley put them 1-0 ahead in their semi-final second leg, and when Eric Abidal saw red after 66 minutes, Guus Hiddink's side looked home and hosed and in line for a repeat of last season's final.
Malouda was wrestled to the ground in the penalty area by a Barca defender but the 'referee' waved the Blues' claims away, a motion that would become a habit during the match.
But with time ticking away, Iniesta struck a devastating shot - Barca's first effort on target in the entire match - that beat Petr Cech and sent them through on the away goals rule to the Rome showpiece against holders United on Wednesday 27 May.
The Blues made a nervous start, with Jose Bosingwa having to hack the ball off the line after a cross was deflected goalwards. But their nerves were soon settled in spectacular fashion as Essien fired in a first-time left-footed volley that crashed in off the underside of Victor Valdes' crossbar after just nine minutes.
Barca finally had an effort on goal when Dani Alves' 35-yard free-kick sailed wide of Petr Cech's goal. But the Blues were soon on the attack again with Didier Drogba's fierce free-kick touched away by Valdes' leg, while John Terry was just a yard off target with a towering header.
Drogba then saw penalty claims waved away by referee Tom Ovrebo after he went down under Abidal's clumsy challenge.
The Spaniards finished the half the stronger, but Chelsea defended resolutely as the interval arrived with no further incident.
But the Blues were soon on the attack after the break, with Nicolas Anelka slipping Drogba in on goal, but Valdes' outstretched boot saved his left-footed effort.
The Ivorian then saw penalty claims waved away once again, but Yaya Toure's challenge in the box appeared good. A rare Barca thrust saw Lionel Messi cut in from the right and unleash a powerful drive that flew high and wide.
But Barca's task was made far harder after 66 minutes when Abidal was harshly shown a straight red card after he clipped Anelka's heels as he burst towards goal.
Chelsea saw another penalty claim waved away when Gerard Pique handled the ball in the area.
But with time ticking away, Iniesta's first-time shot - after Essien had fluffed a clearance - flew into the top corner to spark scenes of jubilation for Barca.
There was still time for Chelsea to see further penalty claims waved away and furious scenes at the final whistle could have further ramifications for the Blues.
But with time ticking away, Iniesta struck a devastating shot - Barca's first effort on target in the entire match - that beat Petr Cech and sent them through on the away goals rule to the Rome showpiece against holders United on Wednesday 27 May.
The Blues made a nervous start, with Jose Bosingwa having to hack the ball off the line after a cross was deflected goalwards. But their nerves were soon settled in spectacular fashion as Essien fired in a first-time left-footed volley that crashed in off the underside of Victor Valdes' crossbar after just nine minutes.
Barca finally had an effort on goal when Dani Alves' 35-yard free-kick sailed wide of Petr Cech's goal. But the Blues were soon on the attack again with Didier Drogba's fierce free-kick touched away by Valdes' leg, while John Terry was just a yard off target with a towering header.
Drogba then saw penalty claims waved away by referee Tom Ovrebo after he went down under Abidal's clumsy challenge.
The Spaniards finished the half the stronger, but Chelsea defended resolutely as the interval arrived with no further incident.
But the Blues were soon on the attack after the break, with Nicolas Anelka slipping Drogba in on goal, but Valdes' outstretched boot saved his left-footed effort.
The Ivorian then saw penalty claims waved away once again, but Yaya Toure's challenge in the box appeared good. A rare Barca thrust saw Lionel Messi cut in from the right and unleash a powerful drive that flew high and wide.
But Barca's task was made far harder after 66 minutes when Abidal was harshly shown a straight red card after he clipped Anelka's heels as he burst towards goal.
Chelsea saw another penalty claim waved away when Gerard Pique handled the ball in the area.
But with time ticking away, Iniesta's first-time shot - after Essien had fluffed a clearance - flew into the top corner to spark scenes of jubilation for Barca.
There was still time for Chelsea to see further penalty claims waved away and furious scenes at the final whistle could have further ramifications for the Blues.