Patrick Bamford scored what looked like the winner on 83 minutes after an incredibly even match, only for Rudy Gestede to equalise for the hosts in the fifth minute of stoppage time.
Boro were on course to go second after Bamford’s left-footed strike from inside the area.
It was Rovers and Gestede who had the last say however, as the Frenchman smashed home his 11th league goal of the season to leave both sides in the play-off zone, close behind the leading pack.
Referee Mark Clattenburg was booed off at the final whistle by the home fans and Middlesbrough manager Aitor Karanka was sent to the stands after his complaints.
But Blackburn returned to Lancashire with a point to prevent Middlesbrough from climbing into the top two.
Middlesbrough, who slipped down to fourth before kick-off because of Ipswich’s win at Charlton, knew that they would have to stop one of the Championship’s other form teams if they were to stand any chance of climbing in to the top two.
Rovers, unbeaten in their previous eight matches, had to make two changes to the side which defeated Leeds. The most notable was Simon Eastwood’s first start in goal since January because Jason Steele, on loan from Middlesbrough, was ineligible to face his parent club.
And he was soon called into action when he had to race out of his area to head clear a dangerous long ball. While the danger soon disappeared that time, he had to make a strong save to his right shortly after when Grant Leadbitter drove powerfully at goal following a probing Lee Tomlin run.
After consecutive draws, Middlesbrough were looking to return to winning ways and started brightly. They were unfortunate not to have a half-time lead and Jelle Vossen thought he had delivered exactly that.
When Bamford’s curling effort from 20 yards was spilled by Eastwood in the six-yard box, Vossen pounced to lift the rebound up over the keeper but as the ball headed for the line it was hooked clear by Shane Duffy. Winger Albert Adomah then shot narrowly wide of the upright.
Blackburn struggled to get out of their own half and Middlesbrough passed the ball around the green shirts confidently, with Karanka’s men regularly creating chances but failing to convert so the visitors remained in contention for something.
Such was Middlesbrough’s dominance in the first half, it was hard to believe that Blackburn were still level after the home side had mustered up an impressive 12 shots in the opening period alone.
Rovers boss Gary Bowyer needed to find a way of getting his forwards more involved after the restart, with neither Jordan Rhodes nor Rudy Gestede touching the ball anywhere near as much he would have liked.
But the second half continued in the same way, with Blackburn happy to allow Middlesbrough to have possession and look for a counter-attack – and the ploy almost worked.
Seconds after Eastwood had denied Bamford at one end, Blackburn broke down the other end and Dimi Konstantopoulos was forced to make his first real save when he dived to his left to parry Markus Olsson’s well-driven effort.
The best save of the lot, though, belonged to Eastwood. The Riverside was left stunned when he somehow scurried across his line, dived left to turn behind a free header from Vossen which was destined for the net following a lovely George Friend delivery.
There was also a save to deny Emilio Nsue’s back post volley and then from Tomlin but, finally, Middlesbrough got the break they needed.
A failure to deal with a corner saw a half clearance drop invitingly for Bamford to power towards goal. It was helped on its way by a deflection, and Eastwood was finally beaten.
Blackburn, however, battled back and Gestede – sporting a nasty bump on his head after an earlier clash – hit the equaliser when Konstantopoulos did not deal with the ball in to his box late on.