Headers from Christian Benteke and Daniel Ayala left the game wide open after the first half but Wilfried Zaha capitalised on George Friend's calamitous error early in the second to give Palace the win.
Boro were left frustrated after a questionable refereeing performance, but an unconvincing attack left the home side always fighting an uphill battle.
Opposition target weak link Stuani
For the second match in a row, Middlesbrough's attack was left toothless and lop-sided due to a lack of menace on the right wing.
Stewart Downing performed well and there were flashes of promise from Viktor Fischer, but Cristhian Stuani was sluggish and unimaginitive for large parts of the game.
He looked unwilling to take on his full-back and his passing game was poor throughout the game, though one curved run into the centre showed the intelligence he can offer. However, Antonio Barragan failed to find him with his low cross.
With the Albert Adomah-Emilio Nsue right-wing partnership gone, Boro need someone to provide the spark and guile that has arguably been missing since the opening day.
Traore cameo suggests rough diamond
Aitor Karanka has said that he hopes to be the man to bring the best out of deadline-day signing Adama Traore, and the evidence of his time on the pitch today shows that the manager's task may be easier than thought.
Granted, Traore was late to release the ball and his final pass was far from perfect, but he had fans off their seats twice in stoppage time with surging runs.
Frighteningly quick with a few deft touches around defenders, Traore has the raw physicality and the pedigree of education to make himself a real fans' favourite, but he needs patience and understanding.
Exciting, direct and incisive, Traore is everything Boro are frequently accused of lacking in the attacking third.
No luck, no excuse
Fans were frustrated by Crystal Palace time-wasting and two strong penalty calls that went ignored as the referee began to lose control of the game, but they had ample time to create a chance to bring the game level.
For all their huffing and puffing, Boro failed to make a clear-cut chance after Alvaro Negredo was denied by Steve Mandanda at the end of the first half.
Over-reliance on Gaston Ramirez is dangerous if he continually has to miss starts after international duty, and Negredo needs more support if he is to shine.
Palace's winner was unlucky, but Boro will have to deal with bad luck, gamesmanship and poor refereeing better than they did against Palace if they are to extend their Premier League stay into a second season.
De Roon return was welcome but untimely
Chasing the game at home with much of the second half to play, it was a strange decision to make a change in holding midfield as Marten de Roon made his comeback from injury.
The change allowed Adam Forshaw more attacking license but it left Karanka with only one change to try and affect the game.
Jordan Rhodes must be wondering if his top-flight chance will ever come. With Negredo frequently subbed off and David Nugent out of the squad, it seemed he would be given minutes at the Riverside today, but he was denied.
Another presence in the penalty area would have given Boro options and allowed their flair players the chance to be more creative. Will he get an opportunity if Boro need a goal at Everton next weekend?
Attacking confidence needed at home
It's a widely-held belief - and a correct one - that if you win at home and draw away, you'll do fine. Attack at home, set up to counter away, that's the theory; but Boro showed little intent to outgun the opposition bar the ten-minute spells at the end of each half.
Middlesbrough are in the Premier League on merit, and they've had a lot of good said about them by pundits and opposition managers alike.
They've been the equal of Stoke City and West Brom, outclassed Sunderland away and arguably matched Crystal Palace, but they don't seem to have a great amount of confidence or swagger in attack.
It's a difficult problem to nail down, and one which could be solved by a lucky goal off Ben Gibson's backside or deflected off an errant seagull. Boro need to evoke the spirit of that Brentford semi-final and #Believe once again.