A penalty by Frank Lampard and a late goal from Raul Meireles helped Chelsea secure a Champions League semi-final place.
But the 2-1 victory on Wednesday (local time) did not come without a scare as Benfica midfielder Javi Garcia's late goal nearly cost the English side.
The victory over the Portuguese outfit sees the Stamford Bridge side continue on the path towards the final in Munich, but they must now overcome the large roadblock of defending champions Barcelona.
Chelsea found themselves on the back foot early as Benfica looked to level the tie, with Nicolas Gaitan posing the threat down the left wing, but the Blues defence stood firm to protect both Petr Cech and their first-leg lead.
Ashley Cole lifted Chelsea after breaking broke into the box but he was barged down by Garcia, leaving the referee Damir Skomina with no option but to point to the spot.
Benfica skipper Maxi Pereira was shown a yellow card, which would cost the full back later on.
Lampard dove the ball under the outstretched arms of keeper Artur to give Di Matteo's side a two-goal lead on aggregate.
Midway through the first half David Luiz allowed his former side to break into the box, allowing Gaitan to race forward, but the Argentinian midfielder's cross was blocked by John Terry.
The Chelsea skipper came to the rescue again a minute later after a good move from a free kick found Axel Witsel at the back post.
He knocked it down for Oscar Cardozo, who was free on the penalty spot, but his drive towards goal was cleared by Terry on the line.
Five minutes before half-time, things went from bad to worse for the Portuguese outfit as Pereira was shown his second yellow card for a lunge on John Obi Mikel.
The visitors came out with a purpose for the second half and were nearly rewarded straight away as a slick passing move saw the ball arrive at the feet of Cardozo, but his strike was superbly tipped round the post by Chelsea stopper Cech.
Chelsea hit back as Torres took Emerson one way, then the other, his strike was deflected by the Benfica defender for a corner.
The English side continued to search out the goal that would ultimately kill the game off as a contest, with both Juan Mata and Torres having strikes, but neither could find a way past Artur.
Mata could have finished off the game as his bursting run into the box was found by Kalou, but the Spanish midfielder's strike could only go across the face of Artur's goal and out for a goal kick to the visitors.
Stamford Bridge, or at least the Chelsea end, went silent as a corner from the left wing found Garcia free in front of goal and from two yards out he headed the ball into the net to give Benfica a glimmer of hope.
But Chelsea faithful need not worry as deep into injury time, with Benfica moving everyone forward the Blues broke and substitute Meireles unleashed an unstoppable strike to send the Blues into the semi-final stage of the Champions League.