After losing at Blackpool six weeks ago, the Lilywhites were looking to make some amends in the visit to the east of the county.
They had much the better of a first half played on a soaking pitch, but didn't have anything to show for that 45 minutes.
Blackburn were much better after the interval and scored their winner nine minutes into the second half, Ben Brereton Diaz guiding home a fine header from Reda Khadra's cross.
They were able to control the second half after that, playing it at their pace and limiting PNE to very little going forward.
That was the big disappointment for the 4,330 travelling North End supporters who would least have hoped for a couple of close calls and good chances to encourage them.
As it was, there was little creativity on show from the Lilywhites as another three points went begging.
North End's starting XI had shown four changes from the side which had drawn with Fulham, three enforced through injury and one voluntary.
Matthew Olosunde, Jordan Storey, Greg Cunningham and Ched Evans came into the team, Tom Barkhuizen, Sepp van den Berg and Andrew Hughes missing because of injury.
Sean Maguire made way for Evans up front, Evans having scored in two goals in two games as a substitute.
Conditions in the first half were awful, the pitch very wet from heavy rain which had fallen since the morning.
In some areas of the pitch the ball didn't run properly because of standing water, it a relief as the rain eased off as the half went on.
North End mastered those conditions far better than Rovers, looking the stronger side.
Alan Browne dragged a low shot wide of the target in the fifth minute having picked out by a fine Evans' pass, conditions underfoot seeing the skipper taking an extra touch than he would have liked to get it under control.
Daniel Iversen fell to his left to fall on a tame shot from John Buckley, that the home side's only real chance of the first half.
North End midfielder Ali McCann sent a shot wide from 20 yards and Emil Riis opened his body up on the edge of the box and curled an effort high over the bar.
Their best first-half chance came in the 34th minute, Ben Whiteman delivering a corner from the right low to the near post.
Evans connected with it and his low shot was parried by Rovers goalkeeper Aynsley Pears who held the ball at the second attempt as Liam Lindsay closed in.
Blackburn manager Tony Mowbray was booked just before half-time for taking his protests about a drop ball too far.
It was the home side who came out of the traps more quickly in the second half and were on top of the game when they took the lead in the 54th minute.
The ball was laid off to Reda Khadra on the left-wing, the loanee bending a cross right-footed into the box,.
Brereton Diaz met it on the corner of the six-yard box and guided a superb header across goal and inside the far post.
It became a struggle for North End from then on in an attacking sense, with Rovers protecting their lead well.
In the 77th minute, McAvoy made a double change, putting on Scott Sinclair and Daniel Johnson for Greg Cunningham and McCann.
That saw a change to 4-3-3 but it didn't have the desired affect.
North End had bits and pieces of pressure in the closing stages although the best chance fell at the other end, Daniel Iversen saving well low down to stop Brereton Diaz scoring a second.
There was a late shout for a penalty when Josh Earl's cross struck the arm of Ryan Nyambe .
But otherwise it was an untidy finish top the game, hopeful balls forward producing little.
Blackburn: Pears, Lenihan, Van Hecke, Wharton, Nyambe, Travis, Rothwell (Edun 85), Pickering, Buckley (Johnson 66), Khadra (Dolan 77), Brererton Diaz. Subs (not used): Davenport, Butterworth, Clarkson, Eastham.
PNE: Iversen, Storey, Lindsay, Cunningham (Sinclair 78), Olosunde (Ledson 82), McCann (Johnson 78), Whiteeman, Browne, Earl, Riis, Evans. Subs (not used): Bauer, Rafferty, Maguire, Hudson.
Referee: Gavin Ward (Surrey)
Attendance: 18,487 (4,330 PNE)
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