The first half belonged to a slick-moving Charlton who could have easily turned round with a three-goal lead. Middlesbrough lifted their game after the break to deservedly extended their unbeaten run to six matches.
Middlesbrough manager Steve McClaren praised Charlton for their first-half tactics, but saluted his own players for their recovery.
When asked what had gone wrong in the first half McClaren replied: "All credit to Charlton, they came with a game plan and played well.
"They man-marked Juninho and kept him quiet in the first half.
"Juninho however, came into the game in the second half and was unlucky not to score. He is used to man-marking. He has had it all his career.
"I thought we were tremendous in the second half. Once we equalised I thought their was only going to be one winner."
Charlton shook the usually reliable Middlesbrough defence with their pace in the first half, Kevin Lisbie missed a glorious chance when somehow he shot over the bar from four yards when it looked easier to put the ball into the net.
Charlton carved out other chance and there was no question they deserved their lead through Jonatan Johansson after 26 minutes.
Middlesbrough struggled to put their game together in this period and were fortunate when Jason Euell missed a great scoring chance just before the break.
It was a different story after the interval. Middlesbrough surged forward with more passion and commitment and suddenly Charlton were hanging on.
Geremi hit the crossbar with a free-kick and Juninho forced a double save from Dean Kiely. Kiely, the visitors' best player, parried his first shot and then darted forward to block the follow up.
Middlesbrough's strong pressure paid off when Malcolm Christie scored his first goal at the Riverside Stadium following his transfer-window signing from Derby County.
In injury time Paul Konchesky struck the crossbar with a free-kick but defeat for Middlesbrough would have been a cruel blow after their second-half performance.
Charlton manager Alan Curbishley praised Radostin Kishishev for his man-marking of Juninho.
Curbishley said: "I thought he did a fantastic job. We won the first half on tactics, but Middlesbrough got into the game in the second half.
"Middlesbrough have a fantastic chairman and the potential to break into the top six. We want to break our record of 52 points. That is our first goal."