The South London side impressed with their teamwork and movement to the delight of their 150 fans who had made the long journey to the north-east.
It is early days but Charlton could push for a place in Europe. Striker Darren Bent, who has made a superb start to the season, is confident. "With the quality of players I've seen at Charlton, Europe is not out of the question," he said in the match programme.
Boro fans had hoped their team would follow up the three-goal demolition of Birmingham City in midweek but they were second best in midfield and lacked firepower.
Mark Viduka, the two-goal match-winning hero at St Andrew's, was well marked by Charlton's organised defence.
Middlesbrough began brightly but were second best overall and there were loud boos from the stands at the final whistle.
Charlton must enjoy playing at the Riverside. After five successive draws on Teesside in previous seasons, they were full value for the three points.
It might have been different for Boro if former Portsmouth striker Yakubu had scored inside two minutes but he headed over the bar from Stewart Downing's left-wing cross.
The Addicks hit back immediately but Bent fired wide. Speedy Denmark international Dennis Rommedahl looked dangerous when he broke down the right but fortunately for Boro his cross was too deep and ran out of play.
There was no question of Charlton sitting back in the hope of snatching a point. They pushed forward at every opportunity and prompted Boro manager Steve McClaren to move to the touchline to urge his players forward.
However, the visitors went ahead through Rommedahl who gave Mark Schwarzer no chance following a pass from the outstanding Danny Murphy.
Luke Young cleared off the goal-line from Middlesbrough defender Franck Queudrue following a goalmouth scramble just before the break.
McClaren gave close season signing Emanuel Pogatetz his introduction to the Premiership when he took over from Queudrue for the second half.
Gaizka Mendieta replaced James Morrison but the former Lazio star was on the field for less than 15 minutes before Massimo Maccarone took over from him. Mendieta must have been injured although there were no obvious signs of a problem.
Charlton continued to look the better side and it was no surprise when Chris Perry put them further ahead with nine minutes left. From Murphy's free-kick the former Tottenham defender managed to squeeze the ball just inside a post.
The goal prompted hundreds of Boro fans to make their way to the exits.
In stoppage time Bent raced through unchallenged to beat Schwarzer with a shot from the edge of the penalty area.
It was the final blow for Middlesbrough and completed an impressive performance by the visitors. Bent has become an instant hero with the Addicks fans after netting four goals in three appearances for his new club following his summer move from Ipswich Town.