Rovers had more than their fair share of chances in the first half but Wes Thomas had headed Blackpool in front by the time Simon Vukcevic rattled the post for the visitors.
Henning Berg's side were unable to muster anything like a similar threat in a second half of few chances, and switched off late on to let former Rangers defender Kirk Broadfoot net a first Seasiders goal.
Appleton has now masterminded two wins from three outings, having begun his tenure as Ian Holloway's replacement with four consecutive draws.
The result moves Blackpool three points and four places above Blackburn, who are floundering in 15th place in the npower Championship having won once during Berg's nine matches at the helm.
Bob Harris enjoyed his second start of the season for Blackpool at left-back in place of the suspended Steven Crainey, while Gary Taylor-Fletcher was named among the substitutes after recovering from a hamstring injury.
Berg sprung a surprise by dropping former England goalkeeper Paul Robinson and naming Jake Kean in his starting XI - one of four changes to the Blackburn side thrashed 4-1 by Cardiff eight days ago as Gael Givet, Colin Kazim-Richards and Vukcevic earned recalls.
Blackpool were perhaps surprised by the sight of on-loan Galatasaray forward Kazim-Richards launching a long-throw in the second minute and Vukcevic was allowed space to fire over.
The visitors were quickest out of the blocks and Seasiders defender Craig Cathcart required a last-ditch challenge to deny Jordan Rhodes from Kazim-Richards' cross, before Matt Gilks made saves in quick succession to thwart Rhodes and Vukcevic.
It was therefore against the run of play when Nathan Delfouneso crossed from the left for Thomas to glance in with the assistance of a statuesque Blackburn defence in the 24th minute.
Dickson Etuhu had a chance to bring Blackburn level after the half hour but shot wide from Josh King's clipped cross as Blackpool failed to fully clear a corner.
Kean was nearly caught out by a clever Tiago Gomes free-kick from the left before Scott Dann produced a vital block to divert an Ince effort at the end of a solo run into the side netting.
But it was almost all-square at the break as Vukcevic rattled the post with a shot on the turn.
Kazim-Richards and Thomas both hobbled back into the action following injury scares during a scrappy start to the second half.
England Under-21 winger Ince appeared the most likely source of extending Blackpool's lead and, after breaking free of the Rovers defence to test Kean low to his right, he exchanged passes with Harris for the latter to fire over in the 65th minute.
Harris managed to extend Kean when the Rovers keeper pushed a rasping free-kick behind, but the points were made safe from the resulting corner.
Gomes' outswinging delivery from the right found Broadfoot to thump home unmarked with nine minutes to play.
Givet thought he had a consolation but was flagged offside before Dann almost compounded Rovers' misery by heading against his own post in stoppage time.