Roberto Di Matteo's side were firm favourites to reach the semi-finals after a 1-0 first-leg win in Lisbon, but they were made to sweat before clinching a 3-1 aggregate success at Stamford Bridge on Wednesday.
Frank Lampard's first half penalty and a red card for Benfica captain Maxi Pereira just before the break should have put Chelsea firmly in control.
But this was a far from convincing performance from the Blues and Javi Garcia's late header made for a few anxious moments before Raul Meireles sealed the victory in stoppage time.
"It was a tough game and having won 1-0 away it presented us with a bit of a conundrum," said Lampard, who was scoring his 22nd Champions League goal.
Frank Lampard scores a penalty against Benfica in their CL game. Photo: AFP
"It is a relief to get through as they're a good side and deserve respect.
"We didn't want to be too gung ho."
Chelsea can now look further to another grudge match with old rivals Barca, who claimed a controversial victory over the Blues at the semi-final stage of Europe's elite club competition in 2009.
That was the most recent in a long line of explosive encounters between the two clubs and Chelsea's sixth semi-final appearance in the last nine years looks certain to reignite the feud.
However, Di Matteo's men will need to improve on some wasteful finishing and careless defending here if they are to stun Barca and book a place in the final in Munich.
"You have to respect Barcelona because they are the best side in the world," said Lampard.
"They will obviously start as favourites but we have a lot of self belief and we believe we can beat them."
Benfica boss Jorge Jesus added: "We've been the better team in both legs and I'm very proud of my players.
"We played with 10 men for the best part of an hour and made Chelsea look ordinary. We were penalised by the referee, unjustly I feel."
Salomon Kalou's late winner last week had put Chelsea in charge and they received a further boost as injuries to Benfica's first-choice centre-halves Jardel and Luisao forced Jesus to deploy midfielder Garcia as a makeshift defender.
Yet Di Matteo had warned Chelsea to guard against complacency as the Portuguese team had scored in all of their European away matches this season.
Chelsea had the ball in the net when Juan Mata fired low past Artur, but the Spaniard's strike was correctly ruled out for offside.
Benfica had been warned but their under-strength defence was creaking and Ashley Cole took full advantage in the 21st minute.
Cole made a perfectly timed run into the penalty area and, although his first touch was a little heavy, the left-back's surge panicked Garcia into a crude block that sent him crashing to the turf.
Referee Damir Skomina pointed to the spot and Lampard, making his 550th Chelsea appearance, stepped up to drill the penalty under Artur's dive.
Benfica's hopes of a miraculous comeback suffered a hammer blow when Pereira, already booked for dissent following the penalty, earned a second yellow card for a studs-up lunge on John Obi Mikel in the 40th minute.
Benfica needed an early goal in the second half to have any chance and they almost got it when Oscar Cardozo's curling effort brought a brilliant stop from Cech.
Di Matteo's team should have been further ahead when Ramires, producing an unwanted candidate for miss of the season, somehow failed to convert Kalou's cross-shot from barely two yards out.
Torres and Mata had chances to kill off Benfica but couldn't finish, yet there was a moment of concern for the hosts as skipper Terry was forced off.
Terry's departure unhinged Chelsea's defence and substitute Yannick Djalo twice went close with a shot and then a header.
When Kalou was denied by Artur it seemed of little consequence, but Garcia set up a tense finale when he rose unmarked to glance a close-range header past Cech from an 85th minute corner.
Chelsea's nerves were showing now, but substitute Meireles finally ended Benfica's spirited show when he broke away and lashed past Artur.