The hosts ensured it was no walk-over for Sam Allardyce's side after they played some good football, but were ultimately denied a cup upset following some ruthless play from Rovers.
A sixth minute strike from David Dunn sent Blackburn on their way and David Hoilett looked to have sealed it with a goal seconds into the second half.
The Gills stormed back when Simeon Jackson tucked away a 70th minute penalty kick, but just four minutes later the two-goal lead was restored as Morten Gamst Pedersen scored direct from a corner kick.
Blackburn went into the match with defeats from their opening two league games and manager Sam Allardyce made seven changes to the side which lost at Sunderland.
Carling Cup progress is very much on Allardyce's agenda and his side made a rampant start.
Just moments before Dunn's opener a brilliant one-handed save from Simon Royce had denied Pedersen after the Norwegian's 25-yard free-kick headed towards the top corner.
Gillingham responded to the early onslaught with some pressure of their own and former Millwall striker Mark McCammon put a header just wide of Jason Brown's goal.
Brown, who was returning to his former side, thwarted the Gills again on 37 minutes as he saved Barry Fuller's curling free-kick and McCammon's follow-up was blocked.
Just 35 seconds after the interval Hoilett pounced from close range, but fellow Canadian Jackson looked to have put Gillingham back into the game.
He was fouled in the box by Zurab Khizanishvili and picked himself up to slot home the penalty kick.
Gillingham's hopes were extinguished just moments later as Pedersen delivered a curling corner-kick that beat everyone and nestled into the bottom corner to seal the win.