The Lancashire side claimed three Premiership points following their Carling Cup quarter-final win in mid week.
Middlesbrough showed more commitment than in the cup tie following a roasting by manager Steve McClaren, but the harsh reality is that they are sliding close to the relegation zone.
Boro have an excellent defensive record in Europe this season, but they had kept only one clean sheet in the Premier League - and that was on the opening day against European champions Liverpool.
Shefki Kuqi was the two-goal matchwinner for a Blackburn side that showed sound defensive qualities throughout the game.
Middlesbrough piled on plenty of pressure but they struggled for a breakthrough against a well-marshalled defence.
Goalkeeper Brad Friedel did not have a serious shot to save in the 90 minutes.
The slide in the league table must be worrying for McClaren, who was booed by a section of the crowd when he stepped into the technical area late in the game.
Blackburn have not enjoyed the best of fortune at the Riverside Stadium over the past ten years, but they certainly have happy memories of their double visit this month.
Manager Mark Hughes must again have been pleased with the overall workrate of his team.
Middlesbrough recalled Gaizka Mendieta after a lengthy absence with a knee injury, while Blackburn had Craig Bellamy on the substitutes bench.
The Blackburn fans taunted the home crowd with chants of "Where were you on Wednesday night?" - a reference to the disappointing Carling Cup attendance.
Middlesbrough had a glorious chance to go ahead after only two minutes. Mark Viduka provided a left-wing cross to the unmarked Yakubu at the far post, but the club's leading scorer headed wide from four yards.
It turned out to be a costly miss.
Middlesbrough showed more puropse and determination compared with the League Cup tie with McClaren urging his players on from the touchline.
Mendieta was booked for showing dissent on one occasion and then wasted a scoring chance when he shot wide from 12 yards.
The combative Robbie Savage was unlucky for Blackburn when his shot went inches past a post with goalkeeper Mark Schwarzer making a despairing dive.
After 38 minutes Blackburn took the lead through Kuqi. Brett Emerton provided a left-wing cross and Kuqi rose high in the air to place the ball into the corner of the net.
Blackburn skipper Andy Todd suffered a leg injury early in the second half. A stretcher was called for, but eventually Todd walked to the touchline with substitute Aaron Mokoena taking his place.
Middlesbrough substitute Adam Johnson took over from Fabio Rochemback, while Blackburn sent Bellamy on for David Bentley.
Shortly after McClaren made a double substitute choice in a desperate bid to save the game. Jason Kennedy took over from Doriva and Jimmy Floyd Hasselbaink replaced Mendieta.
Within a minute hopes of saving the game were dashed when Kuqi scored his second goal. Schwarzer could only parry a Bellamy shot and left Kuqi with a simple chance to score from four yards.
Middlesbrough continued to struggle for a breakthrough and Blackburn came close to increasing their lead in injury time when Schwarzer raced out of the penalty area.
Fortunately for Middlesbrough and in particular Schwarzer, skipper Gareth Southgate cleared from Kuqi.