Yakubu rose high to meet a Stewart Downing corner and send a powerful header past Newcastle United goalkeeper Steve Harper.
The fourth goal of the season by the former Portsmouth player was greeted with a tremendous roar by Middlesbrough fans.
Successive wins over Everton and Newcastle has lifted the gloom on Teesside but another setback for Newcastle increases the fears that Glenn Roeder's side could be in for a long hard winter.
This was not a memorable derby - though Middlesbrough fans may not agree with that verdict!
There was plenty of hard running and effort from both sides but the game was short on quality.
Central defender Jonathan Woodgate returned for Middlesbrough after injury while Harper kept his place in goal for Newcastle after a fitness test.
Middlesbrough began the game as favourites but Newcastle were the livelier side in the early stages, with skipper Scott Parker among those having a crack at goal.
The Magpies could have taken the lead when Antoine Sibierski slipped the ball to £10million signing Obafemi Martins.
The Nigerian got ahead of Emanuel Pogatetz and looked a certain scorer when he lobbed the ball over Mark Schwarzer.
The Australia international had left his goal unguarded in a bid to cut out the danger and was relieved when he saw Martins' lob hit the top of the bar and go out of play.
A lucky let-off for Middlesbrough, who were denied a goal shortly after by a brilliant Harper save from a fierce Downing shot.
Boro had settled down at this stage and a Jason Euell shot was just deflected wide of goal, before Andrew Davies headed wide.
Sibierski was jeered by the home crowd when he lay on the ground after a challenge. But the player was obviously injured and he limped out of the action to be replaced by Shola Ameobi.
Euell shot just wide from 30 yards and then put another effort into the arms of Harper.
There was no question of Newcastle putting up the defensive shutters and seeking a point, with a possible three on the break.
The play was end-to-end with Newcastle creating openings in the Middlesbrough defence.
Neither side, however, had established command by half-time.
Middlesbrough sent on two substitutes immediately after the break.
Robert Huth took over from Andrew Taylor and Fabio Rochemback replaced Mark Viduka.
Manager Gareth Southgate, rather surprisingly, decided on a 4-5-1 formation.
Huth immediately came into action when he blocked a shot by Parker, who was having an industrious game in the visitors' midfield.
A Downing free-kick could have caused problems for Newcastle, but Harper pushed the ball on to a post for a corner.
The goalkeeper could not have had much time to judge the flight of the ball in the crowded goalmouth.
Damien Duff broke from the right into Middlesbrough's penalty area but he could get no power behind his shot.
Yakubu tried a speculative shot at the other end but he was well off the mark. His hit-and-hope shot did not worry Harper.
Parker forced his way into the Middlesbrough penalty area where the ball ran for James Milner to hit a first-time shot that went inches wide of the far post with Schwarzer rooted to the spot.
A goalless draw looked inevitable when Steven Taylor cleared off the goal-line from Rochemback, but Yakubu had other ideas.