A 56th minute goal from Salomon Kalou was all that separated the sides, but the Ivorian turned villain just fifteen minutes later as he dragged down Herita Ilunga in the box to give away the penalty.
However, Petr Cech saved superbly from Mark Noble's effort and the away side held on for a fine victory against their London rivals.
The loss greatly harms West Ham's chances of securing Europa League football next season, and defeat to Chelsea is not what Stamford Bridge old boys Gianfranco Zola and Steve Clarke will have been looking for on the day they agreed new contracts with the Hammers.
Meanwhile, Chelsea will be elated to have taken all three points while managing to rest their key players ahead of the UEFA Champions League clash with Barcelona on Wednesday.
Opening exchangesWith player transfers a constant backdrop to this derby, it was not surprisingly former West Ham man Frank Lampard who created the first chance when he slid the ball through to Florent Malouda in the 16th minute - but the Frenchman dragged his shot wide after racing through.
The away side dominated the early part of the game, but Kieron Dyer - in the starting line-up for the first time since August 2007 - should have given the hosts a lead shortly after, only to shoot tamely at Cech after Diego Tristan had split the Chelsea defence.
The focus then switched back to Lampard once again and with jeers ringing in his ears, the midfielder unleashed a few sighters on Robert Green's goal.
One volley flashed wide, a second went straight at the West Ham goalkeeper and Noble bravely blocked another.
Chelsea were applying the majority of the pressure, but almost fell behind just before the break.
Matthew Upson rose to meet Noble's header and John Obi Mikel was called into action to clear off the line when Tristan prodded the ball towards goal.
BreakthroughDespite the scare though, the visitors were ahead 10 minutes after the restart.
None other than Frank Lampard picked up the ball, wriggled to the byline down the left and floated a cross to the far post, where Kalou took one touch before planting his finish into the empty net for his ninth goal of the season.
Unfortunately Lampard and Terry then proceeded to celebrate in front of the Bobby Moore Stand and missiles were thrown towards them from the crowd - an incident the Football Association could now look at.
With the lead secured, Jose Bosingwa was given a breather just before the hour mark in preparation for Tuesday, while Zola's response to falling behind was replacing Dyer and David Di Michele with Freddie Sears and Radoslav Kovac.
Nicolas Anelka should have doubled the lead when Juliano Belletti sent him through after Upson slipped, with Green rushing out to block the finish, and seconds later Ashley Cole shaved the crossbar after exchanging passes with Malouda.
PenaltyThe Hammers kept on battling though and were given a spot-kick 20 minutes from full-time when Illunga's shirt was pulled back by Kalou in the box.
Noble's penalty was struck well but Cech leapt to his left and tipped away the effort to the great disappointment of the home fans and the West Ham players.
Heads seemed to drop and despite efforts to find the equaliser, the game was beyond West Ham, leaving Chelsea to see out the five minutes of added time and secure a valuable win.
West Ham United
1st Half Goals
Shots on Target
Shots off Target