With a 1-0 advantage from the first leg at the Estadio da Luz, the English side took an early lead in the reverse fixture when Frank Lampard fired home from the penalty spot after 21 minutes.
The visitors were reduced to ten men just before the break as Maximilano Pereira was dismissed for two bookable offences.
Javi Garcia gave the Portuguese outfit hope when he equalised on the night with five minutes remaining, but Raul Meireles sealed a Blues victory with a winner in injury time.
Roberto Di Matteo is glad that his side are through to the last four, but feels that the home team made it difficult for themselves.
“As I said yesterday in the press conference, we expected a difficult game, a hard game, and that proved to be it exactly,” he confessed to Sky Sports.
“We probably made it a little bit more difficult for ourselves by not scoring a second goal, especially in that second half with all those chances.
“That kept them alive and [gave them] hope that they would score a goal and still be in it.
“They moved the ball around very nicely. We didn’t quite keep possession enough as we’d have liked to with the extra man.
“I think the team wasn’t as sparkling as we were hoping it would be. Maybe they were a bit tired.
“But we’re pleased to have won the game and gone through. We deserved it over the two legs,” he concluded.
By Gareth McKnight