The final had appeared to be heading for extra-time as Oscar Cardozo had levelled from the penalty spot just eight minutes after Fernando Torres had put Chelsea ahead on the hour.
But it was won in injury-time as Branislav Ivanovic rose brilliantly to head home a Juan Mata corner to give Chelsea yet more European silverware just 12 months after claiming the Champions League title.
It was a night of disappointment for Benfica as they played their part in a thrilling contest in Holland. The Portuguese outfit were by far the better team in the opening half, and they enjoyed good possession throughout – but they failed to really test Petr Cech.
As early as the second minute Cardozo headed over, whilst Nico Gaitan twice fired wide and Enzo Perez and Eduardo Salvio were constantly probing and driving forward from midfield.
One-time Bolton loanee Rodrigo probably had the best chance of the half when a free-kick was taken short and came into him just six yards out, but he twice lost his footing and missed the chance to test Cech.
Chelsea were limited but Artur had to pull off an exceptional save just before the break when Frank Lampard made a rare foray to the edge of their box and unleashed an archetypal thunderous drive, but the Brazilian managed to tip it over when he looked to be going the wrong way.
Into the second half and the expected reaction from Chelsea did not materialise with Benfica pushing forward in numbers again. Gaitan saw a half-volley fly wide before Cardozo had a header ruled out for offside.
On the hour mark Cech made a good save from Salvio’s back-post header – but from that nobody expected what was to come as Chelsea were ahead within seconds.
Cech threw the ball long for Mata in the centre-circle, he flicked it on and Torres was away, holding off Luisao and going past Artur before finishing clinically.
Chelsea’s lead though lasted just eight minutes. Cesar Azpilicueta handled in the box as substitute Lima flicked the ball on and Cardozo stepped up to hammer the ball past Cech.
Both teams pushed on for the winner and they both had their chances. Cech was at his best as he tipped over a brilliant dipping volley from Cardozo.
Then captain Lampard came within inches of winning it in the final minute of normal time but his stunning effort from 30 yards cannoned back off the bar.
But, just when the game looked to be heading into extra-time, Chelsea won it. Ramires chased down a long ball to win a corner, Mata took it and Ivanovic rose unmarked to head into the corner of the net.
Still there was time for Cardozo to almost be presented with a chance to take the match to extra-time, but he was denied by a great lunge from Gary Cahill and Chelsea celebrated as the full-time whistle went just moments later.