The left winger, who turned 20 just five days ago, converted a low cross from Bonne eight minutes from time at the second attempt as Charlton recorded their first win in 12 games.
Not since October had Lee Bowyer's side tasted victory. Bonne was central to this triumph having scored Charlton's first two goals before supplying the winner for Doughty.
The result meant that Bristol City have now lost four successive Championship games and have dropped out of the promotion picture for now at least.
The opening half-hour which passed with barely a chance worthy of the description.
Famara Diedhiou curled a 12th-minute shot just wide of the Charlton post, while at the other end Bonne swivelled on to a low Deji Oshilaja cross only to see his left-foot shot deflected for a corner.
Naby Sarr glanced a header just wide before the game sprang to life in the closing 10 minutes of the first period.
The breakthrough came five minutes before half-time through a sublime piece of finishing from Bonne.
Boosted by the goal, Charlton pressed for another before half-time. First, Taylor stabbed a shot goalwards following a free-kick. Then, Conor Gallagher's fierce cross caused consternation in the visitors' defence.
Their failure to add to the lead proved costly just 45 seconds into the second half when Andreas Weimann threw himself at a cross from City substitute Niclas Eliasson to guide his header into the far corner of the net.
The Swede's driving runs down the right caused all manner of problems for the home defence. He completed the turnaround on the hour but not before a Sarr header had struck the back of Taylor Moore and looped up onto the City crossbar as Charlton sought to restore their lead.
Again, that escape proved pivotal for the visitors as the ball ricocheted into Eliasson's path for him to steer his shot through the legs of Charlton keeper Dillon Phillips.
It was Bonne who lifted the Charlton spirits once more. His persistence in following in a Taylor flick-on was rewarded 12 minutes from time when he lifted a fierce shot into the roof of the net to give Charlton a deserved point.
That was followed by a cross for Doughty's winner four minutes later. The youngster's first shot was spilled by Bentley allowing Doughty to squeeze home his second effort.