Lee Cattermole, the 18-year-old midfielder, was Boro's match-winner as he scored his first Premiership goal for the Teessiders.
And Boro's young guns, who produced a polished performance, ought to have won by a wider margin as they maintained their fabulous run against City, who have never beaten them in 14 Premiership matches.
While this victory virtually secures Boro's Premiership status, City continued their worrying end of season slide.
This was their fourth straight defeat and hopes of a UEFA Cup place have long since disappeared.
It was all change as City made four alterations from the side which was beaten at Chelsea, with the fit again Georgios Samaras, Trevor Sinclair and Antoine Sibierski all returning.
The visitors had an even more unfamiliar line-up with only four of the players who started in Switzerland three days earlier keeping their place.
The two mid-table teams failed to shine in a dour opening half in which neither goalkeeper was seriously troubled until Boro stole ahead in the 42nd minute.
Up to that point City had marginally the better of the play with Albert Riera twice going close with a well struck free-kick, followed by a drive.
The hosts also had claims for a penalty midway through the half when Darius Vassell was put clean through on goal by Stephen Ireland's slide rule pass, only to tumble in the area with replays suggesting he was shoved by George Boateng.
Boro, who suffered an early blow when Franck Queudrue limped off after nine minutes, never seriously looked like finding a route to goal.
Then suddenly they created a goal out of nothing as Stewart Downing whipped in a pinpoint cross from the left and Cattermole headed home from 12 yards, low to the left of David James.
Cattermole almost doubled Boro's lead early in the second half, only to be denied by a double save from James after he had been put through by Yakubu.
Boro continued to carve out chance after chance with Yakubu coming close on three occasions, while James Morrison was also denied by a super stop from James.
Fabio Rochemback then took centre stage as the Brazilian midfielder had three decent strikes at goal in a nine-minute spell, forcing James to make two decent saves.
City only had fleeting moments when they threatened the Boro goal, although Richard Dunne and Samaras both had headers which flashed narrowly wide.
Indeed, Boro keeper Brad Jones only made one save in the entire match, a header from Micah Richards which replays showed was going wide of the target.
By the end many disappointed City fans had already left Eastlands and those that remained greeted the final whistle with a chorus of boos.