Markus Babbel grabbed a point for Blackburn with his second goal of the game in stoppage time at Ewood Park.
Both his headers were identical, coming from Brett Emerton inswinging corners.
Middlesbrough were left shaking their heads in disbelief at the end after coming from behind to move into the driving seat.
A double blast from Juninho seemed to have secured the points but Babbel had the last word.
Blackburn manager Graeme Souness decided to ring the changes after losing at home to Aston Villa at the weekend.
Martin Taylor, Garry Flitcroft and Nils-Eric Johansson were all drafted in at the expense of Andy Cole, Craig Short and Tugay.
Stewart Downing and Andrew Davies replaced Danny Mills and Massimo Maccarone in the Middlesbrough line-up.
Babbel, on a season-long loan from Liverpool, put Blackburn ahead in the third minute.
He got on the end of Emerton's corner to send a towering header beyond goalkeeper Mark Schwarzer.
It was the German defender's second league goal for the club after arriving on loan from Liverpool.
Blackburn almost added a second in the eighth minute when Taylor got clear of his marker, only for his header to come back off the inside of the post.
Middlesbrough nearly went ahead in their first attack after 21 minutes.
Michael Ricketts forced a superb save from goalkeeper Brad Friedel when he powered in a header following a cross from Downing.
Middlesbrough equalised in the 30th minute after a swift counter-attack that caught the home side cold.
Downing released Ricketts down the left and he played the ball into Juninho, who had timed his run into the box perfectly.
The Brazilian produced a clinical finish, finding the corner with his effort.
Middlesbrough were growing in confidence with Juninho and Boudewijn Zenden always looking for an opening.
Juninho then picked out Gaizka Mendieta but he dragged his shot wide from a good position just before the break.
Blackburn striker Cole was brought on at the start of the second half for the ineffective Yorke.
Alan Mahon, recalled from a loan spell at Ipswich, replaced Johansson, in another switch.
Cole was quickly into the action and saw his effort scrambled away after a flowing move involving Barry Ferguson and Paul Gallagher.
Middlesbrough edged ahead in the 50th minute when Juninho got his second goal of the game.
The little Brazilian is in his third spell with the club but he remains a class act.
He latched on to a clearance from Schwarzer to bend a 20-yard shot around Friedel.
Blackburn midfielder Mahon went close in the 58th minute, his powerful drive going inches wide of the post.
Mahon was looking lively and delivered a good cross into the area but Cole just failed to get a touch.
Then a rare mistake by Middlesbrough defender Gareth Southgate let in Emerton.
The Australian tried his luck when Cole was in a better position and saw his effort beaten away.
Juninho, who had worked his socks off, was replaced by Jonathan Greening in the 74th minute.
Middlesbrough were not content to sit on their lead and went looking for a third goal.
However Blackburn equalised in stoppage time with an action replay of their opening goal when Babbel headed home a corner from Emerton.
The relief around Ewood Park was tangible at the final whistle following that defeat by Villa.
However Blackburn remain dangerously close to the relegation zone - and Souness knows that.Reuse content