Australian international striker Mark Viduka scored the only goal of the game just seconds before the interval to condemn Blues to their ninth away defeat of the season.
Manager Steve Bruce was forced into making several changes from the team that had won against Sunderland last weekend with son Alex replacing the injured Martin Latka at centre-back, Neil Kilkenny coming in for the injured Muzzy Izzet in midfield and Nicky Butt and David Dunn starting the game in place of Jiri Jarosik, who was named amongst the substitutes, and the injured Chris Sutton.
Middlesbrough were without striker Jimmy Hasselbaink who was ruled out with a cold shortly before the game.
Blues 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 then conceded to waste a great chance to give Blues the lead when he headed wide from just six yards out with only Mark Schwarzer to beat.
Yakubu then missed a good chance for the home side 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, and against the run of play, Boro took the lead. Viduka collected a Cattermole pass, controlled the ball beautifully and shot past goalkeeper Maik Taylor and into the net.
Blues, 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 Bruce 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.
Blues were piling on the pressure in bid to pull the game around and only a brilliant block by George Boeteng denied Jaroski in the closing stages.
Blues face a nail-biting finale to the season but have a great opportunity to climb out of the bottom three when they face neighbours West Brom at St Andrew's next weekend.