It was the Lilywhites' first opening-day league win since 2008 and was thoroughly deserved.
After a tight and niggly first-half, Alex Neil's men were the better side in the second half and created a string of good chances.
Tommy Spurr saw a header hit the bar, with Sean Maguire and Callum Robinson going close.
The winner came in the 79th minute after substitute Jordan Hugill was fouled in the box by Tom Lees - Johnson calmly converting from the spot.
Maguire and Darnell Fisher made their competitive debuts, Maguire at the lead of a 4-2-3-1 formation.
Tommy Spurr got the nod to partner Paul Huntington in the centre of defence, with Fisher at right-back and skipper Greg Cunningham on the left.
The early play was something of a slow burner, both sides taking a while to get to grips with the pace of the play.
A 13th minute shot from Alan Browne was charged down on the edge of the box, good approach play from Robinson playing him in.
Ben Pearson got his customary yellow card in the 22nd minute, this one for a bit of a lunge at Fernando Forestieri - later, the Wednesday man followed him into the book for a late challenge on Paul Huntington.
With half an hour gone, Robinson sent a free-kick from 25 yards whistling wide of the post as keeper Keiren Westwood scrambled across his goal.
The best chance of the first half fell Maguire's way in the 40th minute, the Irishman having looked lively throughout.
Getting possession outside the box, he drove down the left hand side of the box and got a shot away with Westwood parried behind at the near post.
At the other end, former PNE loanee Adam Reach dragged a low shot wide from outside the box.
Two minutes into the second half, Greg Cunningham got down the left channel with a powerful run, his cross finding Robinson who could only send a header straight at Westwood.
Good play from Maguire almost brought an opening for Preston in the 54th minute, his low powerful cross from the right pushed out by Westwood, with Lees clearing the lose ball.
Two chances came in quick succession for the hosts as they enjoyed a good spell of pressure.
After an hour, Maguire led a counter-attack from his own half, carrying the ball forward before laying a pass out to the overlapping Robinson.
Taking the ball into his stride, Robinson curled a right-foot shot across goal and just wide of the far post.
Soon after that, Fisher got down the right channel and put in a low cross, one which Maguire slid in to meet and knocked wide of the target.
Hugill joined the action in the 67th minute, replacing Browne.
That substitution saw Maguire move out to the left, Robinson switched into the No.10 role and Daniel Johnson stepped back into midfield next to Pearson.
Former PNE winger Ross Wallace went close for Wednesday within a couple of minutes of joining the action from the bench, driving a shot inches too high after cutting in the right-wing.
Maguire gave way to Paul Gallagher in the 75th minute, his race run after running himself into the ground leading the line.
Gallagher almost helped PNE break the deadlock soon after coming on, his corner met by Spurr who sent a header against the bar, the ball hitting Cunningham as it bounced down before being hacked clear.
Robinson went close after latching on to a Hugill flick-on, his shot appearing to be tipped over by Westwood - only for the referee to award a goalkick.
The breakthrough was made in the 79th minute, Hugill tripped by Lees as he cut into the box on the left.
Referee Tony Harrington pointed straight to the spot, Johnson stepping-up with his stuttering run and calmly sending Westwood the wrong way with the penalty.
Hugill had the ball in the net in the 85th minute but the effort was chalked-off after the striker handled the ball bringing it under control, that earning him a yellow card.
North End saw out five minutes of stoppage-time to secure the three points, earning a standing ovation at the final whistle - that in contrast to the Wednesday who were booed off by their 5,500 travelling supporters.
PNE: Maxwell, Fisher, Huntington, Spurr, Cunningham, Pearson, Browne (Hugill 67), Barkhuizen, Johnson, Robinson, Maguire (Gallagher 75). Subs (not used): Vermijl, Horgan, Davies, May, Rudd.
Wednesday: Westwood, Hunt, Loovens, Lees, Pudil, Boyd (Wallace 67), Hutchinson (Jones 69), Bannan, Reach, Forestieri, Rhodes (Hooper 57). Subs (not used): Fox, Fletcher, Nuhiu, Wildsmith
Referee: Tony Harrington (Hartlepool)
Attendance: 18,267 (5,489)