Bayer Leverkusen 3 Blackburn 2
Shabani Nonda stepped off the bench to keep Blackburn’s UEFA Cup dream alive.
The striker, on loan from Roma, scored his side’s second goal of the game three minutes from time.
It now gives Blackburn a fighting chance of progressing when the second leg is staged at Ewood Park next week.
With David Bentley also finding the target, those away goals could prove vital.
Yet Blackburn were remarkably vulnerable considering they had gone into this first leg game in the round of 32 with a six-match unbeaten run in the competition.
They could have taken the lead in the first minute when Bentley whipped in a cross from the right.
However, the ball skidded away from Jason Roberts on the wet surface and the chance was lost.
Blackburn, however, were trying to play it neat and tidy in difficult conditions and Benni McCarthy took up a good position in the 11th minute.
He tried to pick out Roberts but there was never enough weight on the pass and Leverkusen were able to clear.
McCarthy then got on the end of a cross from Bentley only for his header to drift wide of the post.
Blackburn kept up the pressure and David Dunn played a superb reverse pass to Stephen Warnock in the 16th minute.
The former Liverpool left-back picked out McCarthy but he had strayed marginally offside.
Blackburn were left stunned in the 18th minute when Leverkusen made the breakthrough.
Jan-Ingwer Callsen-Bracker ghosted in at the far post to head home following a free-kick from Bernd Schneider.
Andriy Voronin could have extended their lead in the 24th minute but scuffed his effort off target.
Blackburn carved out a decent chance in the 31st minute when McCarthy got into a good position.
He saw his effort blocked by goalkeeper Jorg Butt with Dunn screaming for the ball inside the six-yard area.
Dunn raised his arms in frustration at what he saw as a clear chance being wasted.
Blackburn had regrouped and Bentley showed good skill to pick out Aaron Mokoena in the 34th minute.
He weighed up his options and tried to place the ball beyond Butt but only succeeded in sending his effort wide of the post.
Blackburn equalised in the 38th minute when Warnock played a short free-kick to Bentley 25 yards out.
He rattled in a powerful shot that took a deflection of Carsten Ramelow to leave Butt stranded.
Leverkusen regained the lead in the 43rd minute when Ramelow’s effort came off the chest of Ryan Nelsen with goalkeeper Brad Friedel out of position.
Dunn squandered a good chance in the 48th minute when he sent a header wide following a cross from Roberts.
Then Schneider cut inside only to send his effort across the face of the goal, much to Blackburn’s relief.
Bentley tried his luck from distance in the 51st minute but saw his effort clear the bar.
Leverkusen went 3-1 ahead in the 56th minute when a clever back heel from Schneider went beyond Friedel after Gonzalo Castro had played him in.
Stefan Kiessling could have extended their lead in the 59th minute but failed to test Friedel.
Blackburn almost conceded a fourth goal in the 80th minute but Friedel did well to block Kiessling’s effort from close range.
Then Nonda threw Blackburn a lifeline with three minutes to go when he rifled a shot home via the underside of the bar.