Jackson nodded in an Astrit Ajdarevic corner from a tight angle at the back post to secure the Addicks' first league win since Boxing Day.
Hard-working Charlton nullified the threat of their rivals from west London, who have now lost three games in a row and are slipping well behind the top two automatic promotion places.
Perhaps with one eye on Monday's FA Cup tie against Sheffield Wednesday, Charlton boss Chris Powell made four changes to his starting line-up with Dorian Dervite, Danny Green, Simon Church and Rhys Wiggins all returning.
Harry Redknapp had to make do without the suspended Joey Barton, so Tom Carroll started in midfield, while Ravel Morrison made his debut after signing on loan from West Ham.
Although QPR played the more intricate and neat football in the early stages, it was Charlton who could have gone ahead after 12 minutes.
Jordan Cousins hit a cracking drive from almost 30 yards, which hit Rob Green's left upright. Reza Ghoochannejhad snatched at the follow-up, which came back off Green's left post with the keeper stranded.
Had Danny Green made a better choice, the Addicks may have had another opportunity but he played a reverse pass when Cousins was far better placed.
Kevin Doyle had a shot blocked by Dorian Dervite and the ball would not fall kindly for him in another R's attack.
Nedum Onuoha went over in the box under a Michael Morrison challenge, but failed to win a penalty.
At the other end, Iran international Ghoochannejhad directed a header from a Wiggins cross straight to Green.
Redknapp tried to shake things up by replacing the ineffective Junior Hoilett with on-loan Manchester United youngster Will Keane.
Moments later Rangers squandered by far their best opening when an unmarked Morrison lashed a 14-yard shot well wide.
Powell responded with a double substitution as Marcus Tudgay made his Charlton debut the day after signing on loan from Nottingham Forest.
The visitors passed up another amazing chance when substitute Modibo Maiga was gifted the ball by the Yohann Thuram-Ulien. After going around the despairing Charlton goalkeeper, the Rangers substitute lost control and the ball went out of play.
And they were made to pay in stoppage time, when Jackson's last-gasp intervention sealed the points for the hosts.