Yakubu's late winner broke Newcastle hearts in the Tyne-Tees derby and gave Middlesbrough their first back-to-back wins of the season.
Yakubu celebrates his winner
The Nigerian powered in a header from Stewart Downing's well-flighted corner to inflict a third successive Premiership defeat on Newcastle.
Obafemi Martins almost put Newcastle ahead when his chip over Boro keeper Mark Schwarzer struck the bar.
Damien Duff's late miss epitomised Newcastle's costly poor finishing.
Robert Huth was the odd man out as Boro boss Gareth Southgate paired two out of his three international central defenders.
Jonathan Woodgate lined up alongside Austrian Emmanuel Pogatetz and, unsurprisingly, the former Newcastle defender was roundly booed by travelling Magpies fans.
Newcastle created good early chances but let themselves down with some powder-puff finishing.
James Milner's cross found its way through to Antoine Sibierski, who failed to get enough purchase on his shot to trouble Schwarzer from 10 yards.
There were signs that Sibierski and Martins were forging a good understanding and Martins should have done better when Sibierski's pass played him in.
Lee Cattermole and Nicky Butt go head-to-head
Sibierski threaded the needle to play Martins in behind the Boro defence and the Nigerian striker cheekily chipped the ball over Schwarzer - only to see his effort bounce on top of the bar.
Newcastle suffered a blow when Sibierski limped off with an ankle injury and the blue touch-paper was obviously damp as this Tyne-Tees derby failed to ignite.
Milner and Duff switched flanks effectively to present Boro's defenders with a different set of problems but there was a lack of devil about Newcastle's strikers as Woodgate and Pogatetz made their physical presence count in their penalty area.
Newcastle's defence had come in for some flak in recent weeks but the back four presented a solid barrier against Boro and, apart from some long-range sighters from Jason Euell, keeper Steven Harper enjoyed a largely untroubled first half.
Boro boss Southgate reshuffled his pack at half time, with Huth and Fabio Rochemback replacing Andrew Taylor and striker Mark Viduka, in an attempt to force Newcastle to change shape.
Harper was called into action as Downing whipped a curling free-kick into the danger zone, the keeper finger-tipping the ball against the post.
It was an afternoon where defenders held sway and, although there was plenty of neat approach play from both sides, there was always a tackle to snap the door shut when play approached either penalty area.
The standard of finishing continued to plummet, with Duff flopping the tamest of shots into Schwarzer's arms after picking his way through, and Euell blasting over from 10 yards after beating Newcastle's offside trap.
Scott Parker's thrust at the heart of the Boro defence popped the ball up for Milner, who pulled Newcastle's clearest chance wide from 12 yards.
Rochemback thought he had put Boro ahead with a first-time shot from Yakubu's pull-back but Steven Taylor appeared as though from a trapdoor to scrape the ball off the line.
Just as the game appeared to be heading for a goalless draw, Boro conjured up a late winner.
Newcastle's vigilant defending relaxed to allow Yakubu to escape his marker and he met Downing's well-flighted corner with a powerful header to score in a third successive Premiership game.
Middlesbrough boss Gareth Southgate on Newcastle's failure to take their chances:
"It's the first time this season we got a touch more luck than we perhaps deserved.
"If it had finished a draw neither side would have complained, but back-to-back wins is a massive lift for us.
"We shouldn't be surprised at winning games like these. This is the standard we should be setting ourselves."
Newcastle manager Glenn Roeder was left to rue his side's profligacy:
"I think we should have had the game wrapped up at half time but we didn't take our chances.
"When that happens it's always in the back of your mind it will come back to haunt you, and it did.
"Their goal was a killer blow at that stage of the game where you don't have enough time to come back."
Middlesbrough: Schwarzer, Davies, Woodgate, Pogatetz, Taylor (Huth 46), Cattermole, Boateng, Euell (Maccarone 77), Downing, Yakubu, Viduka (Rochemback 46).
Subs Not Used: Turnbull, Arca.
Booked: Rochemback, Maccarone.
Goals: Yakubu 85.
Newcastle: Harper, Carr, Moore, Taylor, Ramage, Milner (N'Zogbia 89), Parker, Butt, Duff, Sibierski (Ameobi 30), Martins.
Subs Not Used: Srnicek, Rossi, Bramble.
Ref: M Atkinson (W Yorkshire).