It was their third defeat on the bounce, Mo Barrow's 12th minute header settling the contest in the Royals' favour.
North End struck the woodwork twice, Louis Moult hitting the post with a free-kick shortly after Reading had taken the lead and substitute Sean Maguire headed against the bar in the second half.
Alex Neil's men bossed the second half but too often the final pass or cross didn't reach its intended target.
The goal they conceded was a poor one, Barrow losing his man at the far post to meet a Liam Kelly free-kick which had been flicked on.
That was Reading's only effort on target of the game, that a clinical approach Preston can only dream about at the moment.
Defeat dropped them down to 11th place - the position they have finished in two seasons on the bounce - and PNE are now six points off the play-off pace with only five games to go.
A top-six finish is looking a fading dream, their fortunes having dipped since the international break.
North End's side had shown three changes from the Easter Monday defeat to Derby, Declan Rudd, Billy Bodin and Moult all recalled to the starting XI with Chris Maxwell, Paul Gallagher and Maguire dropping to the bench.
Rudd's inclusion meant another change between the posts - him and Maxwell have been swapped and switched four games running now.
PNE lined-up in a 4-2-3-1, Moult leading the attack with Callum Robinson behind him in the No.10 position.
It must be said that they started shakily, Paul Huntington conceding a free-kick down Reading's right channel after bringing down Sone Aluko inside the first minute.
But the visitors went close to opening the scoring in the third minute, Bodin cutting inside from the right flank and hitting a left-foot shot which keeper Vito Mannone dived to parry - the rebound hitting Moult and bouncing wide.
Reading took a 12th minute lead after Ben Davies' foul on Jon Dadi Bodvarsson gave away a free-kick down Reading's right - Davies was booked.
Liam Kelly delivered the free-kick with pace into the middle, Bodvarsson flicked on and Barrow lost his man - Alan Browne - at the far post to send a header into the roof of the net.
Within two minutes North End were the width of the woodwork away from an equaliser, a foul on Tom Barkhuizen earning them a free-kick a yard outside the box.
Moult took it, his right-foot effort beating Mannone and hitting the top of the post before bouncing behind.
A couple more half chances fell their way, Moult heading a cross from Greg Cunningham over the bar and Browne seeing a shot blocked by Liam Moore's sliding challenge.
In the 43rd minute Barkhuizen's smart turn was the spark for him to set off on a weaving run down the middle which ended with him shooting from 20 yards, Mannone diving to save.
Two minutes into first-half stoppage-time, North End conceded another free-kick in a similar position to the one which had led to the goal.
Leandro Bacuna swung it into the box, Moore meeting at the far post with a header which Rudd tipped against the outside of the post and behind for a corner.
At half-time, Sean Maguire and Tom Clarke replaced Moult and Davies in a double change.
Boosted by the switch, they carved-out two good opportunities in the first five minutes of the second half.
Cunningham's cross from the left side of the box travelled beyond the far post to Bodin who blasted a first--time shot high over the bar when more composure was needed.
Then in the 50th minute, a cross from man-of the-match Bodin was met by Maguire who sent a bullet of a header bouncing against the bar.
Cunningham put a header too high after meeting Bodin's inswinging free-kick from the right-wing.
In the final stages North End threw everything at their hosts but were held at bay in terms of creating clear-cut chances.
A season which was promising so much is beginning to fizzle out just when it matters.
Reading: Mannone, Gunter, Ilori, Moore, Richards (Clement 46), Bacuna, Kelly (Evans 85), Swift, Barrow, Bodvarsson (Martin 71), Aluko. Subs (not used): Ven Den Berg, Kermorgant, Jaakkola, Holmes.
PNE: Rudd, Fisher, Huntington, Davies (Clarke 46), Cunningham, Pearson, Browne, Bodin, Robinson (Harrop 79), Barkhuizen, Moult (Maguire 46). Subs (used): Gallagher, Horgan, Earl, Maxwell.
Referee: Andy Madley (West Yorkshire)
Attendance: 15,501 (704 PNE)