Emma Hayes' side, thrashed by Barca in the final two years ago, knew they had to score in Spain to overturn a 1-0 first leg deficit.
Facing a side who had won their last 19 home games in Europe, Chelsea's task became harder when Caroline Graham Hansen slotted in the opener after a devastating counter-attack in the 63rd minute.
But the Blues responded four minutes later - while the majority of the more than 70,000 fans inside the Nou Camp were still celebrating - when Guro Reiten coolly struck home after Sam Kerr's smart run in behind.
Chelsea pushed for the winner as they still trailed on aggregate but it never came as Barcelona confirmed their place in the final for a third successive year.
It ends Chelsea's pursuit of a Treble but they remain firmly in the Women's Super League title race and will compete with Manchester United for the Women's FA Cup.
Meanwhile, Barcelona head into the final looking to reclaim the crown they lost to Lyon last year. They face the winner of the second semi-final between Arsenal and Wolfsburg, which ended at 2-2 draw in Germany
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