Mark Hughes' side remain unbeaten in the competition and will now avoid a drop-out team from the Champions League. Nancy twice had debutant Johan Lapeyre to thank, but one of Europe's elite may now await the French side, who dropped to second in the table.
Hughes made six changes to the side that lost 3-1 at home to Newcastle on Saturday. Strikers Matt Derbyshire and Paul Gallagher, who haven't started a game in the league this season, were given the nod ahead of Benni McCarthy and Shabani Nonda.
Sergio Peter and Aaron Mokoena started in midfield ahead of Morten Gamst Pedersen and Tugay, while Jay McEveley and Andy Todd returned in place of Michael Gray and the ineligible Stephane Henchoz.
Nancy arrived in Blackburn on the back of a 0-0 draw away to Nice at the weekend and a 3-0 victory at home to UEFA Cup rivals Feyenoord that took them to the top of the group.
The big surprise in Pablo Correa's side was the introduction of goalkeeper Lapeyre, who was making his first ever start in professional football.
On a cold evening in Lancashire, the temperature inside the ground only ever reached fever pitch in an altogether disappointing first half courtesy of the unconventional antics of the young kamikaze keeper.
The visitors had the best share of the chances in the opening period thanks to the pace of frontmen Kim and Issiar Dia.
On four minutes, Kim was played through and went down under the challenge of Brad Friedel, only to be awarded a corner. Seven minutes later, Rovers only half-cleared their lines from a corner on the right and wing-back Frederic Biancalani forced a smart save from the Rovers keeper after firing a low drive through the crowded box.
Rovers' best chance of the half arrived on 22 minutes and they really ought to have taken the lead. Neill supplied a pin-point throughball for Derbyshire. The youngster looked composed, but fired a tame shot straight at the legs of the Nancy keeper.
Four minutes later and Kim showed good speed once again. After outpacing McEveley, he again went down in the box, but again Austrian referee Gerald Lehner was unmoved.
Rovers were dealt a cruel blow when the experienced Todd looked to twist awkwardly and immediately signalled to the bench that he could no longer continue. Irishman Eddie Nolan came on to make his Rovers debut.
The 18-year-old defender looked nervous early on, giving the ball away on several occasions. On 38 minutes, his mistake almost proved costly, as Biancalani intercepted his pass, before firing another powerful left-foot drive straight into the arms of Friedel.
As the half-time whistle approached and, just minutes after completely miscuing a clearance close to the left touchline, Lapayre came flying off his line to deny David Bentley once again. This time his momentum carried him outside his area, but the referee deemed he had released the ball just in time.
A minute later, Kim avoided the challenge of Neill to run clear through on goal and, with only the keeper to beat, the Brazilian's curling shot struck the base of Friedel's left-hand post and McEveley got back to bravely block Michael Chretien's fierce drive on the follow-up.
The Ligue One side continued where they left off at the start of the second half and should have taken the lead just seven minutes in. Some sloppy defending from Neill allowed in Dia. The striker laid the ball square to the unmarked Pascal Berenguer, but the Frenchmen's mistimed shot was cleared off the line by the retreating Neill.
The Aussie international was again wasteful in possession three minutes later, this time chipping the ball straight to Kim. The Brazilian looked to be inside the area when he went down under the challenge of McEveley, but the official awarded a free-kick less than a yard outside.
Lapeyre pulled off his second important save of the night on 59 minutes, tipping Bentley's sweet right-foot volley over the bar, after the England Under-21 international had teed himself up 25 yards out from goal.
A disappointing final half-hour to the game again came to life with just minutes left on the clock. Substitute Pedersen almost got on the end of McEveley's deep cross on 89 minutes, before Rovers stole the victory in the second minute of time added on.
A corner from the left came all the way over to Bentley on the right wing. The former Arsenal man picked out Neill in the centre with a floated left-foot cross, and the skipper chested the ball down before firing past a flat-footed defence into the bottom right-hand corner of the net.