Jamie Ward and Craig Bryson provided the cutting edge for the Rams as Steve McClaren's men carried on their excellent run of form.
The Rams have lost just once in the 10 games for which former England manager McClaren has been in charge, after taking over from Nigel Clough, but had to show all their defensive qualities to keep Charlton at bay.
Ward scored the 32nd-minute opener and Bryson added a second three minutes from time to inflict a fifth defeat in a row on the Addicks, who hover just above the bottom three.
Charlton's home form has been poor this season with just two wins but they went at Derby from the off, with the visiting defence having to concede a string of free-kicks.
Danny Green curled in good crosses, although no red-shirted player could make clean contact, and he had a long-range free-kick tipped over the bar by Rams goalkeeper Lee Grant.
Home captain Michael Morrison - leading the team in the absence of the suspended Johnnie Jackson - tried his luck with a 30-yard drive but Grant got behind it safely.
Dale Stephens volleyed over the bar from a Bradley Pritchard cross, while Derby skipper Richard Keogh made a vital tackle to thwart Yann Kermorgant's run towards goal.
But the harsh reality is Charlton are the lowest-scoring side in the Championship, while Derby have scored more than anyone, and failing to make their dominance count cost the Addicks dearly.
McClaren's Derby went ahead, entirely against the run of play, when Ward's free-kick took a wicked deflection and left Charlton goalkeeper Ben Alnwick wrong-footed.
Dorian Dervite had conceded the foul on Chris Martin 25 yards out from the centre of goal, to give Ward his opportunity.
Alnwick made a full-length save to deny Bryson as Derby seized the momentum following the goal.
Chris Powell's home side started the second half as they did the first though, and Stephens was inches away from levelling with a low 20-yard effort.
Morrison got the ball caught in his feet and failed to find the net from six yards, and Derby countered.
Ward hit the crossbar from 14 yards after good play from Chris Martin who pulled the ball back for him.
Powell livened up his attack by introducing Simon Church and Callum Harriott in place of Green and Pritchard after 65 minutes.
Morrison again went close for Charlton but his header from a Kermorgant cross drifted wide.
Grant made a solid save to deny Church who managed to penetrate the Derby back-line after a neat ball through by Cameron Stewart.
Powell gambled by throwing on another striker in Marvin Sordell five minutes from the end but it backfired two minutes later when the Rams grabbed their second goal.
Midfielder Bryson took advantage of the space left by Charlton going forward and snatched his ninth goal of the season.