Although Boro are very much on the up this result would have set the alarm bells ringing for the Londoners who have now only won once in their last eight Premiership outings.
After their midweek Carling Cup defeat to neighbours Crystal Palace, it wasn't only the pitch-side announcer who was dropped. Alan Curbishley axed five players and big summer signing Francis Jeffers couldn't even get a place on the bench.
It made little difference to another poor Charlton performance and it came as no surprise when Boro took the lead with a slightly fortuitous goal.
Charlton goalkeeper Dean Kiely cleared the ball straight to Stewart Downing. His cross was met by Jimmy Floyd Hasselbaink whose shot was going wide until it was deflected into the net off Talal El Karkouri, although the former Chelsea player will claim the strike.
In a half of few chances Charlton's only worthwhile goal efforts came from a couple of free-kicks, Mark Schwarzer doing well to tip over El Karkouri's effort.
The second half had barely started when Charlton equalised. Jason Euell's defence-splitting throughball allowed Jonatan Johansson to beat the offside trap and beat the advancing Schwarzer.
Hasselbaink should have put Boro in front but delayed his shot and allowed Kiely to save.
But the visitors quickly gained the initiative as they sliced through the home defence. Mark Viduka's pass found Boudewijn Zenden and the Dutchman finished with a sweet strike inside the post.
Charlton's Achilles heel this season has been their away form which has seen them take just one point from five matches, but they were previously unbeaten at home in the Premiership.
The pressure from their poor away form is now affecting their confidence at home, and Boro were never in too much danger of conceding another goal. Johansson had a couple of weak shots saved as the home side tamely slid to defeat.
MAN OF THE MATCH: Chris Riggott (Middlesbrough) – The former Derby man was a rock at the heart of the Boro defence as he continues to keep Ugo Ehiogu out of the starting line-up.