The champions seemed on course to make it 12 out of 12 in the league at home on the strength of Eidur Gudjohnsen's 18th-minute goal, despite operating at a pedestrian pace against their mid-table London rivals.
However, poor defending allowed striker Bent, signed from Everton on Tuesday for two million pounds, to head a 59th-minute equaliser.
When defender Ricardo Carvalho was sent off 10 minutes from time for a second booking, it was clearly not Chelsea's day.
It was the first time the leaders had failed to win a home league game since a 0-0 draw with Arsenal in April, but Sunday's draw did nothing to change the destination of this year's title.
Their point moved them to 62, 17 ahead of Manchester United (45), who host third-placed Liverpool (44) later.
Charlton also won at Stamford Bridge, on penalties after a 1-1 draw, in the League Cup last October. They climb one place to 11th on 29 points.
Despite the slip-up, Mourinho dwelled on the positives of his side's record when he spoke to reporters.
"When you arrive at the end of January and you lose your first points at home I think it's fantastic," he said.
"I know the (league) record we have with two draws and one defeat is amazing and no defeats at home is unbelievable. So this day had to arrive and I'm happy with the team and the situation.
"Ask Manchester United and Liverpool if they would like to swap places."
TOP FORM
Chelsea were on top from the start and took the lead when Hernan Crespo's goal-bound header was parried by goalkeeper Thomas Myhre and Eidur Gudjohnsen reacted quickly to touch it over the line.
Charlton's Radostin Kishishev hacked it clear but the linesman correctly flagged that the ball had crossed the line.
On a poor playing surface Chelsea were unable to turn their possession into clear chances against a team who had lost their last four away league games.
The champions continued to stroll through without much urgency and paid the price on the hour.
Darren Ambrose picked out Bent and the unmarked striker, on as a 40th-minute substitute, looped a header over the stranded Petr Cech.
Chelsea manager Jose Mourinho reacted immediately by throwing on Shaun Wright-Phillips and, for his debut, Portugal midfielder Nuno Maniche.
It was Charlton, lifted by the goal, who looked the more dangerous and they should have taken all three points in the 83rd minute when headers by Marcus and Darren Bent sent Ambrose through, only for Cech to block his low shot.
