Matty Blair scored in injury-time to deny Charlton a fourth win in five league games.
Patrick Bauer’s first-half header looked to be enough to seal the points in a one-sided game where the Addicks should have scored more.
However, Blair’s 94th-minute header broke Charlton hearts.
A win would have moved Charlton into the top six after Bradford drew against relegation-threatened Bury.
Karl Robinson made two changes to the side that lost to Oxford United last week with Bauer and Ben Reeves coming in for Harry Lennon and Stephy Mavididi. Meanwhile, Nicky Ajose was included in a Charlton matchday squad for the first time in 13 months.
Doncaster threatened on five minutes when Andy Boyle headed James Coppinger’s corner wide.
Tariqe Fosu, who looked menacing whenever he had the ball, beat three Doncaster players to cross for Josh Magennis, and the striker would have had a tap-in if it wasn't for Boyle’s vital clearance.
But Charlton took an 18th-minute lead from the resulting corner thanks to Bauer, who netted his third goal of the season after connecting with Jake Forster-Caskey’s corner.
Former Millwall striker John Marquis could have hit back for Donny instantly, however, he shot straight at Ben Amos following a good passing move.
Charlton should have doubled their lead just before the break after a slick counter-attack ended with Magennis and Mark Marshall having goal-bound efforts blocked.
The Addicks started the second-half in the same manner in which they played the first - on the front foot.
Marshall’s excellent crossfield pass found Jay Dasilva, who cut the ball back to Fosu in the box. The winger created space for himself with his quick feet and saw his powerful drive saved by Ian Lawlor.
The Doncaster goalkeeper was busy once again when he did well to deny Reeves’ fierce volley.
Fosu wasted a glorious chance to kill the game off late on when he rounded Lawlor, but couldn't get a shot away thanks to Tom Anderson’s last-ditch tackle.
That moment came back to haunt Charlton as Blair’s late header ruined the visitors’ day.
Charlton XI: Amos, Solly, Bauer, Konsa, Dasilva (Lennon, 90), Kashi, Forster-Caskey, Marshall, Reeves (Jackson, 88), Fosu (Kaikai, 82), Magennis.
Subs not used: Phillips, Aribo, Zyro, Ajose.
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