The Frenchman slammed home after failing to score direct from the penalty spot. His left-footed rebound was scuffed into the net but no-one cared, well that is not true because Charlton boss Alan Curbishley was livid.
And he had good reason, Frank Lampard, not for the first time this season, surged forward and latched on to a pass from Joe Cole. The England midfielder realising he could not reach the ball decided to take a dive.
Not only was he not touched by Jonathan Fortune, but he hit the ground from outside the penalty area.
Referee Mike Riley however saw things differently and pointed to the spot to the utter dismay of the Charlton players.
Makelele, was given the ball by regular penalty taker Lampard and seconds later the game was over, match won for the Blues and Championship medals but minutes away from being handed out.
Charlton must feel aggrieved as they set out their stall to defend, defend and then defend some more and for 90 minutes, their tactics worked.
They took full advantage of the fact Chelsea boss Jose Mourinho would rest players, goalkeeper Petr Cech replaced by Carlo Cudicini and striker Didier Drogba not even on the bench.
He also was without his two influential wingmen, Arjen Robben and Damien Duff.
The Addicks took a leaf out of Liverpool's books in midweek and tried to stifle the life out of Chelsea and hope to grab a goal on the breakaway.
Charlton's best efforts fell to centre-back Jonathan Fortune - the big man was on the end of slick Charlton attack on 29 minutes, but aimlessly half-volleyed over Cudicini's bar from six yards out.
His second effort showed good skill, as on 41 minutes, a deft turn and shot eight yards out saw a low left-footer go agonisingly wide of the Chelsea goal.
Charlton had just two more efforts on goal - a 10th minute Bryan Hughes run into the area saw his right-footed shot on target, but Cudicini was excellent to tip the ball away for a corner.
Cudicini demonstrated his excellent reflexes to pull off a similar save from Matt Holland on 65 minutes.
But Chelsea had by far the better of the chances and they were more clear-cut.
As early as the eight minute, Chelsea signalled their intent. A Lampard corner was headed on to goal by Ricardo Carvalho, but the ball was deflected away by Jonatan Johansson.
Lampard missed a sitter of a header on 23 minutes after good set-up play by William Gallas on the left. Lampard failed to keep his header down, instead seeing it sail over the Charlton crossbar.
Five minutes later, man of the match Joe Cole got his first taste of goal action, but his left-footer was well held by Stephan Andersen.
Cole was again the most effective forward and was unlucky to see a curler of a right-footer spin wide after he produced a fine run into the penalty area.
Cole hit the woodwork on 35 minutes when a 20-yard blaster was deflected by Andersen on to the crossbar.
It seemed as if Chelsea were going to see their last home game of the season descend into a scoreless draw.
The crossbar came to the aid of Charlton on 53 minutes when a Glen Johnson cross was met by skipper John Terry, but again the woodwork denied the Premiership winners the goal their play deserved.
But fate conspired against Charlton and Riley's incorrect decision resulted in the last-gasp penalty and ultimate defeat.
Man of the Match: Joe Cole - Produced one of his more productive performances of the season. Always the focal point of Chelsea's attacks, he was unlucky not to score, but the woodwork intervened. His ball control was impeccable and passing supreme.