Rovers were hard done by because there was no doubt that Bolton striker El Hadji Diouf made a meal of a challenge by Brad Friedel.
It looked a clear case of diving - not the first time the striker has been accused - but referee Steve Bennett was taken in and awarded a penalty.
Just to rub salt into Blackburn's wounds Friedel saved the initial kick from Diouf but was helpless as the striker converted the rebound.
Rovers were incensed that Diouf was even on the pitch to take the kick, not just for the dive, but also for the first half elbow on Andy Todd for which he somehow escaped with a yellow card.
It was a poor game with too many misplaced passes and badly timed tackles but there was no way that Rovers, who gave a debut to Robbie Savage, deserved to lose.
Morten Gamst Pedersen was the first player to get a shot at goal, his eighth-minute effort bringing a good save from Jussi Jaaskelainen.
The Bolton keeper did even better five minutes later to push aside a goal bound effort from Lucas Neill.
A Pedersen volley disappeared over the Bolton bar as Blackburn began to get the upper hand and David Thompson was only inches away with a header.
It wasn't until the 55th minute that Bolton managed a shot at goal - an effort from substitute Kevin Davies that cleared the bar.
It was ironic that Bolton should settle matters at a time when Rovers were having a decent spell, but the goal finally decided this frantic Lancashire derby was controversial in the extreme.