Middlesbrough's victory took them 11 points clear of trouble as they achieved their first Premiership away win of the season and their first in 16 matches on the road.
The result was a bitter blow for Charlton manager Alan Pardew who described the game as his team's first cup final of the season.
But lacking injured talisman Darren Bent, they lacked punch up front and their defence once again caved in under pressure and they have now conceded 43 goals already this season.
With confidence at rock bottom their frailty was evident as they collapsed in the second half as Boro scored twice in four minutes to make sure of the points.
The home side took the lead when Jimmy Floyd Hasselbaink scored against his former club to net his first Premiership goal for Charlton in three months.
Matt Holland's long ball was mis-headed by Emanuel Pogatetz sending the ball into Hasselbaink's path and his volley hit the ground before looping into the net.
Charlton looked to be in reasonable control of the game but conceded a goal at the worst possible moment just seconds before the half-time whistle.
They felt they should have had a free-kick in Middlesbrough's build up to the goal when Andy Reid appeared to be fouled but the referee allowed the game to continue and Mark Viduka played in Lee Cattermole for the youngster to shoot low into the net.
A terrible mistake in the Charlton defence after 64 minutes gifted Boro a second goal. Hermann Hreidarsson tried to chest Stewart Downing's cross back to his goalkeeper but made a complete hash of the clearance and the ball fell to Julio Arca who easily found the net.
Four minutes later it was all over for Charlton when Yakubu cut in and unleashed a great shot from outside the area which flashed into the top corner.
In desperation Pardew sent on three substitutes and they might have pulled a goal back when Holland's fine low show was turned away for a corner by Mark Schwarzer.
Pardew - Charlton's third manager of the season - knew he had a tough task on his hands to keep the Addicks in the top-flight and the Boro match was a must win game for his team if they had any hopes of avoiding the drop.
Championship football now looks a near certainty at The Valley next season unless Pardew can produce the biggest escape act of his career.
Middlesbrough boss Gareth Southgate had asked his side to be more adventurous away from home and they certainly responded with this performance and result as he got the better of Pardew who was a former playing colleague at Crystal Palace.