It took a late Raul Meireles goal to settle Chelsea nerves after a game drifting towards a comfortable if unspectacular home win was brought back to life by an 84th minute Benfica goal.
It was a much stronger performance by the Lisbon club than had been witnessed on their home turf but after Frank Lampard had put his side ahead from the penalty spot and the visitors had been reduced to 10 men by a sending off for Maxi Pereira, Chelsea were well on course for the semi-finals.
Roberto Di Matteo's men should have put the tie beyond all doubt in the second half but missed a handful of good chances and were then punished for poor set-piece defending by a Benfica side that had always carried a threat. Javi Garcia made it 1-1.
Fortunately with the Portuguese outfit committing men forward in stoppage time for the goal that would have sent them into the semi-final, Chelsea landed the sucker punch.
There was just one change from the weekend win at Villa. Ramires, such a problem to Benfica left-back Emerson in the first leg, returned with Daniel Sturridge making way. Scorer in Portugal Salomon Kalou was on the other flank and Fernando Torres continued in attack. Didier Drogba was fit enough to return to the bench, while David Luiz, who came off on Saturday, was able to start.
In contrast, Benfica were missing both centre-backs from the first leg, captain Luisão and Jardel, so Emerson moved across to the middle and Spanish World Cup winner Joan Capdevila came in on the left of their defence. Former Chelsea man Nemanja Matic was handed a start in midfield.
Chelsea had to defend almost non-stop for the first four minutes as Benfica, attacking the Shed End containing their fans, started with a high tempo. There were important block tackles from Lampard and John Terry on the edge of our area before we eventually took the ball inside the opposition half.
The Blues won our first corner on seven minutes, flicked on to David Luiz in space who rifled a shot goalwards, blocked well by the leg of Capdevila.
We threatened to cut through the Portuguese side on the break soon after but Mata got his angles wrong in attempting to find Torres ahead of him. Mata had the ball in the net seconds later, but had run offside in the move.
The Slovenian ref wasn't slow to whistle up physical contact and on 18 minutes he produced a yellow card for the first time. David Luiz had anticipated well, nipping between Oscar Cardozo and the ball and receiving a kick on the ankle from the Benfica striker as a reward.
A minute later the ref was reaching for his card again, this time in the aftermath of awarding Chelsea a penalty. Cole had just taken down a lofted ball forward when he was bundled to the floor by stand-in centre-back Garcia. Bruno Cesar and Maxi Pereira were booked in the aftermath.
The keeper went the correct way with his dive but Lampard found the bottom corner with his spot kick for his 22nd Champions League goal. Chelsea were 2-0 up on aggregate with 20 minutes of the second leg played.
Five minutes later, there was more vulnerability at the back from Benfica when everyone missed a Cech long punt. Torres ran clear but wide and then picked out no one in blue with his ball across.
Aimar made it three Benfica bookings for dissent and four overall before his side came close to a goal with that rarest of sights in the modern game, a free-kick routine. Initially played out wide, it was eventually nodded down to Carodozo who beat Cech with his shot but Terry blocked on the line and Ivanovic cleared.
Ivanovic was the first Chelsea name in the book on 37 minutes for a trip on Gaitan after the previously high-standard Mikel and Ramires conspired to give away the ball. The Benfica free-kick that followed was played straight into the Chelsea wall.
The cards kept coming on this stop-start evening and when Pereira slid his studs into Mikel's shin, he saw his second yellow and had to walk early down the tunnel.
Ramires was cautioned for a late tackle on Bruno Cesar who was now right-back. Prior to that the Brazilian made what was one of very few first-half Chelsea chances, firing across the area but just out of the reach of Torres and Kalou.
Three minutes after the restart, Cech needed to produce his best save of the game after Cardozo swung a leg at a bouncing ball and sent it towards the top corner. Our keeper dived, extended one of those long arms and sent the ball over.
A minute later and up the other end, Ramires somehow missed the chance for a Chelsea second after Kalou had deceived Bruno Cesar at the far post and shot for the opposite corner. His Brazilian team-mate slid in and made contact but the player rather than the ball ended up in the net.
Torres turned sharply inside the area and looked to have placed his shot inside the post but it was deflected just wide and Kalou headed a Mata cross wide. Chelsea had started the second half much better than the first.
A second goal looked like it was coming but Artur saved acrobatically from Mata before Benfica made a surprising substitution, taking off Cardozo and bringing on Oliveira. Chelsea made a sub too, replacing Terry with Cahill. The skipper went straight down the tunnel for treatment.
Chelsea's grip on the half loosened a little when Ivanovic misdirected a header and another substitute, Djalo, had a goal-bound shot deflected wide by Cahill, but then Kalou, who was seeing plenty of ball on the left, should have scored but couldn't beat the keeper from close-range. Against a side with reduced numbers and inexperience in the heart of their defence, the feeling was the Chelsea attackers should be doing better.
Mata was next to shoot wide, having been teed-up by a skilful Kalou pass but although there was more of a goal threat about Chelsea this half, we were looking less secure at the back. Djalo headed a cross just over Cech's crossbar.
On 74 minutes, MIkel spread the play out to Cole who crossed low. Kalou controlled it, spun but shot wide again.
The card count was much reduced in the second half and Cole and David Luiz managed to avoid bookings that would have ruled them out of the first game against Barcelona, but Mikel did pick up a caution for tripping Matic.
On 84 minutes came the Benfica goal. Cech had only just saved well to prevent Djalo heading in but from the corner that followed, Garcia ran unmarked to flick home with his head.
Drogba was quickly introduced for Torres in attempt to keep more of the ball but Chelsea had not been the same defensively since Terry went off.
Happily, inside the four minutes of stoppage time that were played, another substitute, Meireles was able to charge from his own half against a depleted Benfica backline, stretched even further by a supporting run from Ramires. The Portuguese international, once again much booed by the Benfica fans, smashed the ball into the net and Chelsea were through.
A repeat of the 2009 Champions League semi-final awaits, although this time Barcelona visit us first.
Chelsea (4-2-3-1): Cech; Ivanovic, David Luiz, Terry (c) (Cahill 59), Cole; Mikel, Lampard; Ramires, Mata (Meireles 79), Kalou; Torres (Drogba 88).
Unused subs Turnbull, Ferreira, Essien, Sturridge.
Scorers Lampard pen 20, Meireles 90+2.
Booked Ivanovic 37, Ramires 43, Mikel 78.
Benfica (4-1-3-2): Artur; Pereira (c), Garcia, Emerson, Capdevila; Matic; Bruno César (Rodrigo 72), Witsel, Gaitán (Djalo 61); Cardozo (Oliveira 56), Aimar.
Unused subs Eduardo, Almeida, Nolito, Saviola.
Scorer Garcia 84.
Sent off Pereira 39 (2 yellows).
Booked Cardozo 18, Bruno Cesar 19, Pereira 19, Aimar 27.
Referee Domir Skomina from Slovenia.