Boro are now clear of a relegation spot and could even finish in the top half of the table.
However, Birmingham face a nail-biting finale to the season and have a crunch game against neighbours West Brom next weekend.
Sunderland and Portsmouth are favourites for the drop with the battle for the third spot between the two Midland rivals. Australian international Mark Viduka was Middlesbrough's hero with a goal on the stroke of half-time.
It was a triumphant return to the first team for the striker who a month ago, following the 4-0 home defeat to Aston Villa, suffered abuse from fans during and after the game.
Middlesbrough were without striker Jimmy Hasselbaink who was ruled out with a cold shortly before the game.
His absence solved a selection dilemma for manager Steve McClaren as it would have been difficult to leave the Dutch striker out on recent form.
Birmingham, who were desperate to avenge a 3-0 defeat earlier in the season, were without the injured Chris Sutton in attack.
City had not collected a single point on their previous three visits to the Riverside Stadium. In fact it is over 20 years since they won on Teesside with Boro's former Ayresome Park ground also not being a happy hunting place for them.
There was little flair in the opening stages with neither side showing any impressive form although Lee Cattermole shot just wide for Boro after a good run.
Boro were forced to make an early change when Stuart Parnaby was injured and substitute Andrew Davies took over.
Emile Heskey wasted an early chance for Birmingham when he headed wide when Mark Schwarzer appeared to be beaten.
For Boro, leading scorer Yakubu missed a glorious chance when he shot wide from six yards.
There was no sign of a repeat of last season's eight-goal spectacular between the teams at the Riverside Stadium.
Just before the break however Boro's fans had something to cheer when Viduka collected a Cattermole pass, controlled the ball beautifully and shot past goalkeeper Maik Taylor and into the net.
Birmingham, inevitably, began the second half in an attacking mood and only a brilliant reflex save by Schwarzer prevented an equaliser by David Dunn.
Shortly afterwards Dunn was replaced by Dudley Campbell and City also introduced Jiri Jarosik for Neil Kilkenny. Jarosik tried a shot after he had been on the field for only two minutes but his poor effort only hit a corner flag.
Birmingham were piling on the pressure in bid to pull the game around with manager Steve Bruce anxiously patrolling the touchline.
George Boateng made a brilliant block to deny Jaroski in the closing stages as Boro held on to clinch three vital points.
The win puts Middlesbrough in good heart for the UEFA Cup tie against AS Roma at the Riverside Stadium on Thursday night.