Skipper Gareth Southgate has virtually given up hope of a Champions League place next May, but Boro could qualify for Europe via the UEFA Cup once again.
Middlesbrough survived a frantic finale, in which midfielder Ray Parlour was dismissed for his second bookable offence, but they deserved the points.
Blackburn, despite strong second-half pressure, failed to create one clear-cut chance.
There was a pre-match collection for the Brian Clough Memorial Fund.
There are plans to erect a statue of the former footballing legend in his home town and fund organiser John McPartland was confident of generous support.
Middlesbrough were hit by injuries and illness to several recognised first-team players and included no fewer than six youngsters from their Academy in a 16-man squad.
Malcolm Christie made his first home appearance in 15 months after recovering from a broken leg.
Blackburn hoped to recover from their midweek defeat by Chelsea and avenge a 4-0 defeat at their home ground in October.
Parlour was booked in the early minutes for a heavy challenge on Robbie Savage.
Following a Joseph-Desire Job cross from the right wing, Christie headed into the net, but the flag had been raised for offside. Stewart Downing hit the sidenetting with a right-shot from just inside the penalty area.
Shortly after in the 35th minute, Downing was involved in the matchwinning goal from Frenchman Franck Queudrue.
The impressive defender collected Downing's pass to cut inside the penalty area and leave Brad Friedel helpless with a strong shot.
Middlesbrough played the more enterprising football in the first half and should have increased their lead before the break. James Morrison had an excellent chance to create an opening for the unmarked Christie, but the youngster shot straight at Friedel.
Blackburn disappointed in the first half and failed to test home goalkeeper Mark Schwarzer, who has shown a lack of confidence in recent games.
Savage was having a relatively quiet came in the Blackburn side. It looked as though the controversial midfielder was feeling the effects of heavy tackles early in the game.
Blackburn, however, showed more spirit after the break. The industrious Paul Dickov had a header tipped over the ball by Schwarzer and later had a strong penalty claim turned down.
Blackburn switched to more attacking 4-4-2 formation in a bid to pull the game round.
Middlesbrough struggled at this stage of the game. They needed a lift from their fans but there was little response at the time when the home team needed encouragement.
Middlesbrough sub Danny Graham took over from Christie, who was clearly lacking in match fitness after his 15-month absence.
Dutch international Boudewijn Zenden headed just over the bar for Middlesbrough, while Blackburn were angry when central defender Michael Reiziger sent Dickov tumbling with a challenge in the box.
Dicjov looked distraught when the referee waved aside penalty claims.
Blackburn stepped up the pressure in a frantic finale but Middlesbrough held on.
In the final minutes Parlour was sent off for his second bookable offence, the former Arsenal midfielder foolishly kicking the ball away and he will miss next week's visit to Bolton Wanderers.
Middlesbrough boss Steve McClaren was jubilant over the performance of his young side.
He said: "We deserved to win, the attitude of the players from the first whistle was excellent. We finished with five academy players on the pitch.
"Their attitude was absolutely tremendous. We should have been one or two goals up at half-time.
"We had very good chances to kill Blackburn off. Everyone played superbly particularly to grab a clean sheet. A clean sheet was important and we worked hard for it."
When questioned over the penalty claim, he added: "The linesman and the referee were very close and they never saw it."
When asked about Parlour's sending-off: "It was a rash decision and a stupid one. The referee had no choice but to send Parlour off.
"Anybody who can play central midfield should give me a call in midweek."
Rovers boss Mark Hughes was annoyed over being denied a penalty and the performance of match officials.
The former Wales boss said: "We felt it was a penalty, the assistant referee was wrong all game and did not help the referee at all. The big decisions are the ones the referee and the assistant have to make and we suffered.
"There was a big call on the penalty and we never got it.
"We have suffered three 1-0 defeats and gone close in all these games. My players were not as lively as I expected in the first half, but Middlesbrough were sharp and closed us down very quickly.
"In the second half we asked more questions, but we didn't really create a clear cut chance. We need a goalscorer, someone to put the ball in the net."
Man of the Match: Franck Queudrue - Apart from his all-important goal, the Frenchman gave a sterling performance in defence when Blackburn piled on the second-half pressure.