Robbie Keane reduced the deficit from the penalty spot but, despite a late surge, it is Chelsea who will take on Blackburn in the semi-final.
There was a cup tie crackle inside the Lane before and once the game got underway, with our team setting up in a similar fashion to the system employed at Stamford Bridge - Aaron Lennon operating just behind the two front men.
A Berbatov back-heel nearly opened corridor of uncertainty in the Chelsea backline for Keane to exploit, before Dimitar Berbatov himself made Petc Cech stretch towards the top corner to gather his first header of the game at the five minute mark.
A period of pressure without testing Cech followed before Chelsea pinged the ball around with some authority - Michael Ballack very much pulling the strings - and the most threatening move ending with Shaun Wright-Phillips drilling over from around 20 yards.
The game was frenetic, but the football of a high quality, with excitement and tension hanging in the cold night air as we waiting for events to take their course. Berbatov was not too far off thrusting his head onto a zipped in cross from Jenas, the opportunity coming as a result of Lennon hunting defenders and not permitting them to dwell on the ball.
It was passion and drive with limited creativity as we closed in towards the break with neither side particularly looking likely to break the deadlock.
There was a purposeful beginning to the second half and Pascal Chimbonda nearly profitted from a Jenas corner and Michael Dawson flick-on - Cech saving well. The lively Steed Malbranque then had the Czech working again with a low drive to his right.
The momentum was well and truly with us at this point in time, Jenas was skipping past Ashley Cole with ease, while Lennon and the excellent Lee Young-Pyo were combining well to provide a significant danger from the left.
Amid the pressure, Chelsea did what they do and scored a goal out of next to nothing. Andriy Shevchenko cut in from the right of the area - losing Malbranque in the process - and arrowed an inswinging drive into the top corner of the net with 54 minutes on the clock.
It was two on the hour when Didier Drogba cleverly chested into the path of Wright-Phillips and former Manchester City man delivered a dipping volley beyond the despairing reach of Paul Robinson.
The next move was to introduce Jermain Defoe for Malbranque, but the team appeared to be in collective shock over getting caught with two sucker punches, while Chelsea seemed intent on simply killing the game off by breaking up play and ensuring that a flow did not return to proceedings.
There came a lifeline on 78 minutes wheen Berbatov was felled by Ricardo Carvalho and a penalty was awarded - although no red card was shown despite the central defender being the last man.
Keane was cool after delays and sent Cech the wrong way with a stroked finish to the right.
There was, of course, a big late push for a leveller, but Chelsea stood firm and snatched the spoils.
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Two goals in six second half minutes against the run of play proved too tall an order to overcome as we exited the FA Cup against Chelsea at the Lane.A pretty even first half was followed by a spate of one-way traffic early in the second half and a breakthrough looked on the cards until the visitors landed a devastating couple of counter punches - in truth, superb goals from Andriy Shevchenko and Shaun Wright-Phillips.