Defeat in Turkey last week gave the second leg more of an edge than many had anticipated and Fener began with some hope of an upset.
Then Chelsea took the lead they sought, a goal that took them ahead on the away goals rule and allowed them to relax.
It was Michael Ballack who rose at the near post to head home a right-wing free-kick with just three minutes of football played, lifting the pre-match pressure on Avram Grant's side.
Just one goal from the away side would have been enough to put pressure back on Chelsea, who would then require a further two goals to win, but at no point did this game become that exciting.
Joe Cole almost gave Chelsea a two-goal cushion just two minutes after Ballack's opener, when Salomon Kalou broke down the left and crossed low to Cole at the near post, but his prodded shot thumped the post of Volkan Demirel's goal.
Fenerbahce were gifted some luck when Carlo Cudicini injured his right leg when taking a goal-kick, forcing his exit just 26 minutes in. Chelsea were suddenly down to their third-choice goalkeeper, Hilario, and looked a little exposed.
Diego Lugano had a chance to test the new goalie five minutes later, but his free header, following a deep, lofted free-kick, drifted a foot wide of Hilario's left-hand post.
Yet it said a lot when Fener finally forced the Portuguese into a save, 55 minutes after he entered the game.
An initial block from a low, bouncing shot was followed up by a sharp parry off Colin Kazim-Richards' swerving, 20-yard drive, but even that was well within his limits.
Chelsea themselves failed to test Volkan in the visitors' goal, but they were comfortable with a slow, passing game and scored a second only when the Turkish side began pressing for an equaliser.
Michael Essien showed strength and skill on the right wing as he cut into the area and crossed low for Frank Lampard to finish from four yards out.
It came 87 minutes into the match and ended Fener's hopes. They looked toothless for the most part in attack and a second goal killed off their slim hopes of a late upset.
Chelsea were happy to breeze into a semi-final encounter with Liverpool without ever getting out of second gear.
They have two weeks to prepare for the first leg with their English rivals, a game that will surely test them more than Fenerbahce did.