The Ivory Coast international, who recently signed a new deal with the club, converted either side of the interval having missed several earlier opportunities to break the deadlock.
Frank Lampard ensured Carlo Ancelotti's men continued their 100 per cent record in Group D with his 133rd career goal for the Blues, moving him ahead of Jimmy Greaves to fifth outright in the club's list of all-time scorers, before Luis Perea's last-gasp own goal.
Out-of-form Atletico were a threat in the first period but faded in the second as the set-piece problems which blighted the Blues in their defeat at Aston Villa were not repeated, with weekend culprit Ricardo Carvalho dropped to the bench.
The defeat will heap further pressure on the visitors' under-pressure coach Abel Resino, with the Spanish side facing an early exit from the competition with just one point to show from their opening three fixtures.
There were less than 60 seconds on the clock when Michael Essien released Juliano Belletti down the right flank, but the full-back elected to shoot when Kalou was well placed awaiting a cross in the six-yard box.
Diego Forlan warmed Petr Cech's hands with a shot from distance, before forcing the Blues goalkeeper into a smart save at his near post with a diving header from Simao's clever cross.
FlappedSergio Aguero should have given Resino's side the lead as he was allowed to burst clear despite a strong suspicion of offside, but drove his shot beyond Cech and into the side-netting.
The Blues thought they had gone ahead in the 13th minute when young goalkeeper Sergio Asenjo flapped horribly at a curling Lampard free-kick from 30 yards out, only for the effort to be ruled out with the assistant referee flagging for offside against Kalou.
And the flag was up again seconds later as the Blues cut their way through the heart of the Atletico defence thanks to Deco's deft touch, although Kalou was a relieved man on this occasion with the Ivory Coast international missing badly from Michael Ballack's square pass.
Asenjo produced an excellent stop in the 35th minute, diving to his right to push away a shot from Kalou which took a wicked deflection, with the Blues forward unable to convert at the back post after John Terry's powerful header from the resulting corner.
Kalou finally made the breakthrough in the 41st minute when he fired home from close range after England team-mates Lampard and Ashley Cole combined well for the left-back to provide a low cross across the six-yard box.
BlisteringNicolas Anelka had the first chance of the second period with a blistering drive from the edge of the box which Asenjo could only palm away before the defence scrambled clear.
But the goalkeeper could do nothing moments later when Kalou lost his marker to head firmly into the bottom corner from Lampard's well-flighted corner from the left.
Aguero had the opportunity to reduce the deficit soon after as he raced onto Forlan's flick, only to dwell on the ball in an attempt to make Cech commit himself, with Terry getting back to cover and the goalkeeper then saving low down.
Chelsea continued to press and Lampard made it 3-0 in the 69th minute with a low, bouncing effort from outside the box which beat Asenjo at his near post.
Atletico still posed an occasional threat going forward with substitute Maxi Rodriguez showing quick feet to trick his way through the defence only to roll his shot agonisingly wide with Aguero unable to get a touch.
Cech, who looked shaky at times as he elected to punch rather than catch, saved well with his feet in the closing moments with Maxi Rodriguez again denied having found some space on the right side of Chelsea's penalty area.
There was still time for Chelsea to grab a fourth with Perea glancing substitute Florent Malouda's curling free-kick beyond his own goalkeeper in the first minute of added time.
ChelseaTeam StatisticsAtl?co de Madrid4Goals011st Half Goals05Shots on Target55Shots off Target62Blocked Shots03Corners313Fouls2012Offsides21Yellow Cards20Red Cards077.4Passing Success72.514Tackles2478.6Tackles Success66.755.8Possession44.253.6Territorial Advantage46.4