Chelsea doubled their aggregate advantage when Frank Lampard scored a 21st-minute penalty and their grip on the game tightened five minutes before halftime when Benfica skipper Maxi Pereira was sent off for a second yellow card after a lunge.
Javi Garcia headed in from close range on 85 minutes to prompt a nervous finale for the Londoners before Raul Meireles struck in stoppage time.
Roberto Di Matteo's team have now reached the semifinal for the sixth time in the last nine seasons.