With striker Didier Drogba sitting out the final game of his three-match UEFA ban, his Ivory Coast team mate Kalou grabbed his chance to impress with goals either side of halftime to put his side in charge.
Kalou's strikes deflated the struggling Spanish side before Frank Lampard's shot and a stoppage time own goal by Luis Perea completed a third victory from three matches for Chelsea in Group D.
Carlo Ancelotti's side, who went down at Aston Villa on Saturday to lose the lead in the Premier League, have nine points to second-placed Porto's six. Atletico are bottom with one point and face the prospect of elimination.
Kalou, who recently signed a new contract, plays third fiddle behind Drogba and Nicolas Anelka at Stamford Bridge but underlined his importance to the squad with an all-action performance that could have netted him a hat-trick.
"Drogba is still Drogba," Kalou told reporters. "It's not an insult to be behind him and Anelka because they are two of the best strikers in the world right now. But I'm pleased to get on the pitch and take my opportunity and do my best.
"We have proved that even without our main striker we have the character to win without him. But he will be back next time and that is very important for Chelsea even though its hard to accept if you are not playing."
TERRIBLE MISS
Kalou, playing alongside Anelka in front of Chelsea's diamond midfield, took a while to warm to the task and was guilty of a terrible miss early on when he dragged a shot wide after being played in by Michael Ballack.
Atletico, who have started the Spanish season poorly, matched Chelsea for most of the first half, particularly in a lively opening spell when Uruguay striker Diego Forlan looked menacing. Twice he tried his luck from distance and also forced an acrobatic save from Chelsea keeper Petr Cech.
His striking Argentine partner Sergio Aguero wasted Atletico's best chance when he rolled Branislav Ivanovic easily but shot wastefully into the side-netting.
Atletico always looked vulnerable at the back and fell behind after 41 minutes when Lampard sent Ashley Cole scuttling down the left and his low cross gave Kalou the perfect chance to make amends for his earlier miss.
Seven minutes after halftime Kalou doubled the lead when he sprang high to head Lampard's deep corner past the exposed Sergio Asenjo who was given little help by his defenders.
Aguero then wasted another chance when he dithered too long after being sent clear. As Chelsea took complete control, Lampard rifled in his side's third to snap a 10-game sequence without a goal for the England midfielder.
"I'm happy for Lampard but I think it's important that Lampard is not just about scoring goals," Ancelotti said. "He is very unselfish and works for 90 minutes for the team."
Atletico's miserable night was complete in stoppage time when Perea got the final touch to an inswinging free-kick.
"I think it was one of those bitter tastes of football," under-fire Atletico coach Abel Resino told reporters. "We had as many chances as Chelsea but the ball wasn't going for us."
