New Tottenham boss Juande Ramos saw Christopher Samba smash an injury-time winner as Blackburn registered their fourth successive win.
Spurs had taken the lead on 49 minutes when Robbie Keane scored from the penalty spot after Aaron Lennon had been brought down inside the area.
Blackburn equalised on 60 minutes through Benni McCarthy's deflected 18-yard shot off Michael Dawson.
And the visitors secured the three points with Samba's last-minute strike.
Ramos, who was confirmed as Tottenham manager on Saturday night, sat between chairman Daniel Levy and sporting director Damien Comolli in the directors' box, as Clive Allen looked after the team pitchside.
And the Spaniard will have plenty of work to do if he is to tighten the second worst defence in the Premier League and lift Spurs out of the bottom three.
Much of the fans' frustrations were centred on Levy, who dismissed Martin Jol after the 2-1 defeat to Getafe in the Uefa Cup on Thursday.
Blackburn had goalkeeper Brad Friedel to thank for a string of saves which continually frustrated the home side's best attacking moves.
Spurs made two changes from Thursday, with Keane starting alongside Dimitar Berbatov up front while Dawson slotted into the centre of defence in place of Anthony Gardner.
Blackburn boss Mark Hughes named an unchanged side and it was the visitors who had the first genuine attempt at goal on nine minutes.
David Bentley cut inside on the edge of the box to leave left-back Young-pyo Lee stranded, but, after doing the hard work, the former Arsenal man's shot sailed harmlessly past Radek Cerny's right-hand post.
Spurs attempted to adopt an expansive passing game to exploit Lennon's pace on the right wing, but were continually closed down in midfield by Blackburn, with Robbie Savage proving particularly effective.
The best opportunity of the first half fell to Lennon, who latched on precise defence-splitting pass from Steed Malbranque on 19 minutes, but the England international could not slot the ball past the on-rushing Friedel.
The keeper was once again in the thick of it a minute later, this time palming away Keane's free header for another corner.
Blackburn suffered a blow just before the interval when a knee injury ended Savage's contribution to the game, with Hughes bringing on Aaron Mokoena for the Wales international.
With caretaker manager Allen's half-time team talk ringing in their ears, Spurs took the lead when Lennon shifted a gear to burn past full-back Stephen Warnock, who brought down the winger inside the box.
Referee Rob Styles immediately pointed to the spot and despite the protestations of the Blackburn players, up stepped Keane to fire past Friedel on 49 minutes.
The goal reinforced Spurs' attacking ambition - intuitive interplay on 58 minutes between Keane and Berbatov on the edge of the box put through Lee, who was denied by another excellent stop from Friedel.
However, Blackburn's persistence was rewarded two minutes later when McCarthy created an extra yard of space on the edge of the box and his shot deflected off Michael Dawson's toes, enabling the ball to loop agonisingly over the despairing Radek Cerny.
Despite the setback Spurs continued to push forward and create chances - Friedel once again kept the visitors in the game when he tipped over Berbatov's header on 66 minutes.
Allen continued to push for the winner, replacing Malbranque with record signing Darren Bent and bringing on Jermaine Defoe for Berbatov, but neither man could make the decisive contribution.
But it was centre-back Samba who had the final say - smashing home Roque Santa Cruz's pass from the edge of the box in the last minute of the match.
Spurs caretaker boss Clive Allen: "We're frustrated that we conceded so late in the game, but I am delighted with the response of the players. "I thought we took the initiative in the second half but it's not the result we wanted.
"It's a bad result but I didn't think it was a poor performance. There was confidence about the way we played, we created opportunities to score, which was promising.
