The home side raced into a two-goal lead as Elliot Bennett volleyed home before Danny Graham coolly finished from close range.
Yann Kermorgant pulled one back for the visitors midway through the first half with a superbly taken free-kick.
With time running out Simeon Jackson tapped-in from close range to seal the win for Blackburn.
Having sat comfortably in mid-table for most of the season, both sides had nothing but pride to play for going into the final game of the season.
Despite this, outgoing Blackburn manager Paul Lambert's side started wonderfully as Bennett and Graham gave the Ewood Park faithful two goals to celebrate.
Both teams pressed for goals in a high octane encounter but it was Reading who broke through as Kermorgant blasted home a free-kick from 25-yards out to reduce the deficit.
As the visitors continued to press for a leveller the home side's Jordi Gomez fed Jackson a simple tap-in to kill off the game at the death.
The result meant Blackburn finished in 15th place in the Championship whilst opponents Reading end the season two places behind in 17th position.
Blackburn manager Paul Lambert: "All credit to the players. To be fair we should have been five or six up in that first half.
"I can't ask any more from them. They gave us everything they had and it's a lot of the same guys that went week in, week out for us. We finished the season strongly which was important.
"I've got nothing but good things to say about the club and the players. There are some good players and I think they need help to sustain a challenge in this division."
Reading manager Brian McDermott: "It sums up where we've been in the last couple of years. We've got a lot of work to do, we know that.
"We have got to get the blend right, the chemistry right. We haven't got that right at the moment and that's not just been today. It's been a couple of years at least."
Blackburn comfortably beat Reading in Paul Lambert's last game in charge of Rovers.