Leverkusen had used all their European experience to leave Rovers facing elimination with the match poised to finish 3-1 in their favour.
Jan-Ingwer Callsen-Bracker, Carsten Ramelow and Bernd Schneider were on the mark for the classy German side before the DR Congo striker popped up at the death to hand Rovers a timely boost ahead of next week's second leg.
Rovers boss Mark Hughes was denied the services of Morten Gamst Pedersen and Robbie Savage and the absence of the injured duo appeared to be a major blow as the visitors struggled to cope with an experienced Leverkusen line-up at times during the match.
Jason Roberts made his first start since October after recovering from a broken foot and strike-partner Benni McCarthy should have fired Rovers into a first minute lead but completely missed his kick when presented with an easy opportunity six yards out by David Bentley.
That miss was to prove costly as the home side steadily found their feet and broke the deadlock after 18 minutes.
Defender Callsen-Bracker ghosted in on the back post behind the sleeping McCarthy and headed Schneider's deep free-kick beyond Brad Freidel from point-blank range.
Blackburn regrouped and Bentley fired them level six minutes before the half-time interval.
The lively midfielder crashed a 20-yard low free-kick beyond Hans-Jorg Butt after the ball took a heavy deflection which left the goalkeeper flat-footed.
However, Blackburn's joy was short-lived as Ramelow restored Leverkusen's advantage on the stroke of half-time when his 30-yard drive took a deflection off the chest of the unlucky Ryan Nelsen and left Friedel helpless.
Rovers continued to press in the early stages of the second half but they were undone by a moment of class from veteran midfielder Schneider.
Gonzalo Castro broke down the right and sent over a low cross which the former Germany international impudently flicked past Friedel with the ball rolling over the line after bouncing off the inside of the far post.
Hughes sent on Nonda for the tiring Roberts with 20 minutes left and the arrival of the substitute had the desired effect.
With time running out, Aaron Mokoena won a header in the box and Nonda crashed a rising volley into the back of the net from eight yards.