Earlier, Nuno Gomes's first goal in English football was cancelled out by Leicester striker Jamie Vardy.
The result saw Blackburn move into third place in the Championship table.
The visitors had started the brighter, and were denied an early lead when former England goalkeeper Paul Robinson produced a stunning save to keep out David Nugent's header.
But, against the run of play, Portuguese veteran Gomes dispatched a Jason Lowe cross into the bottom corner of the goal just after the half hour mark.
Leicester responded to falling behind, and Nugent was denied an equaliser either side of the half-time whistle before Vardy - who scored 34 goals for Fleetwood last season - found the back of the net after nipping in front of a hesitant Scott Dann to finish from 12 yards.
An assistant's flag then ruled out a superb Vardy header as Leicester pushed for a first away win of the season.
But it was Pedersen who was to prove the difference with his right-footed finish from the edge of the penalty area.
Blackburn boss Steve Kean on Pedersen's goal celebration:
"It is a little bit tongue in cheek and dressing room banter.
"I don't know where he got that from or if he pre-planned it with our kitman but it should be taken the way it's meant to be.
"I felt at certain times when you have the quality we have in the side, if you have a Gomes or Pedersen with the technical ability they have, they can produce something special."
Leicester boss Nigel Pearson:
"The officials have to make themselves accountable for the decisions they make. They got key decisions wrong.
"Their first goal where they have a man clearly standing in front of Schmeichel. They're either both onside or offside. Vardy is clearly onside.
"Unfortunately they try and clarify things each year but I'm not sure there is clarity in regard to that.
"I think all in all our performances have been very positive and we were certainly worth a win today."
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