Frank Lampard's 21st-minute penalty appeared to calm the home side's nerves after weathering an early storm, as did the dismissal of the visitors' stand-in captain Maxi Pereira just before the break.
But a powerful header from a corner by Javi Garcia with five minutes remaining saw a touch of anxiety creep back into the game, until substitute Raul Meireles lashed home the winner on the night in stoppage time to make sure there would be no dramatic turn-around.
Roberto Di Matteo's side will now meet Barcelona for the right to take on either Real Madrid or Bayern Munich in the final at the latter's own Allianz Arena in May, a semi-final fixture which comes three seasons after the Blues' controversial exit to the Catalan outfit in this competition.
The 1-0 win last week at Estadio da Luz meant that the onus was on the Portuguese club to make something happen in London – a fact the Blues exposed by granting their opponents plenty of space to punch themselves out.
They had to be resolute at the back, however, especially during a tough early period as the visitors came at them as expected: Nicolas Gaitan and Pablo Aimar had early efforts closed down, as did their former employee David Luiz at the other end.
Chelsea’s patience began to reap benefits, and with Benfica makeshift at the back there were numerous openings on the counter-attack, including when Juan Mata had the ball in the net on 12 minutes only for his effort to be ruled out by a belated offside flag.
The key moment came on 20, however, when Ashley Cole burst into the box from out of nowhere to collect a pass only to be barged down, off the ball, by Garcia.
Slovenian official Damir Skomina pointed to the spot, and Pereira and Bruno Cesar received bookings for protesting the decision before Lampard just about squeaked the spot kick under the frame of Artur.
As frustrated as the away side were becoming, they continued to attack with style and Oscar Cardozo’s strike had to be cleared off the line by skipper John Terry from a set piece.
Jorge Jesus’s men continued to collect silly bookings in the meantime, and the one five minutes before the break would be the most costly: it was Pereira’s second following a lunge on John Obi Mikel, and left a bigger mountain to climb.
A frantic opening to the second period saw Cardozo force a fantastic one-handed parry from Petr Cech with a curling drive at the end of a wonderful passing move, moments before another ex-Eagle Ramires somehow failed to convert a tap-in to Salomon Kalou’s square pass from a yard out.
Mata and Fernando Torres came close as the hosts continued to hunt for a safe margin, before the former slipped Kalou into a one-on-one on the left-hand side of the area on 66 minutes, only for Artur to make the block.
Rather than return the favour for the ex-Valencia man, Kalou ended up stealing a promising chance off the toes of Mata by mistake with a quarter hour left, putting his own effort wide on the turn.
And as the visitors, who had looked ready to concede for a fair chunk of play beforehand, won a corner in the 85th minute and Garcia left marker Luiz in the dust to rise superbly and head home a lifeline.
Another goal for Benfica and Chelsea would be out on the away goals rule, but substitute Nelson Oliveira wasted a fantastic opportunity in the 88th by going for goal himself instead of playing in Aimar or fellow replacement Yannick Djalo.
It came down to another cameo man to have the final say, as Meireles – one of just three Portuguese to feature, all of whom came off the bench – surged forward on the break in the second of four minutes added on at the end and sent an unstoppable drive into the roof of Artur’s net.