Chelsea crashed to their first Premiership loss since November - and their heaviest under Jose Mourinho - as struggling Boro were boosted.
Rochemback is mobbed after scoring his first goal for Boro
The leaders conceded after only 78 seconds when Fabio Rochemback capitalised on lax defending.
Boro extended their lead in first-half stoppage time when Stewart Downing's speculative shot ended up in the net.
And they saved their best for last - Yakubu muscling his way past John Terry before striking low into the corner.
Back in October Boro had humbled Manchester United 4-1 at home, but given they had lost 4-0 at home to Aston Villa only last weekend this result was nothing short of remarkable.
The only disappointment for Boro was that Mark Viduka left the Riverside before the start of the game after discovering he had been named as a substitute.
Not that Boro manager Steve McClaren would have regretted his decision to field Yakubu as a lone striker.
That decision was fully vindicated as the Nigerian's strength and speed unsettled the Chelsea defence, playing a part in Rochemback's goal and then scoring himself with a fine individual effort.
It was the heaviest defeat in the 20-month reign of Mourinho - and the joint-biggest loss of his whole managerial career, with a 3-0 setback for Porto in 2002 and a similar defeat with Benfica in 2000 the previous lowlights.
The manner of this loss was even more surprising given Chelsea had only conceded just 13 goals before Saturday.
But there was no sign of that defensive discipline in the second minute when Rochemback dispossessed Michael Essien.
The Brazilian played a one-two with Yakubu, before weaving his way past a Terry tackle and then hitting a shot that Cech really should have saved.
Rochemback nearly claimed a second goal late in the game, but his rising shot was superbly turned away by Cech.
Nothing went right for Chelsea and early on they had to make a defensive readjustment when William Gallas limped off, with Essien having to drop back to fill in at left-back.
Just before the interval Essien managed to get forward from his defensive position to hit a swerving shot that deceived Mark Schwarzer, who was unable to hold the ball.
Hernan Crespo pounced on the rebound and looked certain to score before Schwarzer somehow got one hand on the ball to deflect it away to safety.
Just before the interval the game began to slip further away from Chelsea after Downing manoeuvred his way into the box and hit a low shot that ended up in the net after going through the legs of Terry and Gaizka Mendieta.
On 68 minutes Yakubu capped a fine individual display, leaving Carvalho and Terry trailing in his wake, before unleashing a shot past Cech.
Chelsea's miserable day was completed when substitute Carlton Cole's volley came back off the bar.
Middlesbrough boss Steve McClaren:
"A week is a long time in politics and even longer in football at times. We have had quite an eventful couple of months.
"But credit to the players for this win. Through all the criticism, all the performances and the results, we have always stuck together.
"There has always been a great spirit and it is just rewards today."
Chelsea boss Jose Mourinho:
"When you lose, it is always a bad day, especially when you don't lose a lot.
"In my time at Chelsea, this is the third defeat in the Premiership and you can say it was the worst.
"We lost to Manchester City and didn't deserve it, we lost at Manchester United and didn't deserve it. We lost today 3-0 - and we deserved it."
Middlesbrough: Schwarzer, Parnaby, Riggott, Southgate, Pogatetz, Morrison (Boateng 39), Mendieta (Davies 90), Doriva, Rochemback, Downing, Yakubu (Hasselbaink 90).
Subs Not Used: Jones, Maccarone.
Goals: Rochemback 2, Downing 45, Yakubu 68.
Chelsea: Cech, Geremi (Carlton Cole 45), Ricardo Carvalho, Terry, Gallas (Maniche 17), Gudjohnsen, Essien, Lampard, Robben, Crespo, Joe Cole (Wright-Phillips 45).
Subs Not Used: Cudicini, Huth.
Booked: Terry, Gudjohnsen, Ricardo Carvalho.
Ref: S Bennett (Kent).