A 79th minute penalty from Daniel Johnson gave PNE the three points in front of a bumper Deepdale crowd of 18,267.
North End boss Neil said: "My emotion is one of delight.
"I thought the players did great, I thought we were better than Sheffield Wednesday in pretty much every aspect - we out-fought them, out-played them and we deserved to win the game.
"The players applied themselves really well, I wasn't surprised we were better than Sheffield Wednesday because I have worked with these lads for the best part of a month.
"The application they show every day in training is something they showed today, they work their socks off.
"We have some good quality players, the guys who came off the bench made a real impact too.
"From a manager's point of view, you can't really ask for much more than that.
"If we continue to perform like that, we will be fine."
The Lilywhites had carved-out some decent chances before Johnson's winner, one of those seeing Tommy Spurr send a header against the bar.
Neil said: "When we had the amount of pressure we did, you hope a goal would come.
"Thankfully for us we got enough chances and managed to convert one, albeit that was a penalty.
"We had enough in the game and should and could have scored more."
North End's penalty was awarded after Jordan Hugill was tripped by Wednesday centre-half Tom Lee.
Hugill, subjected of a second bid from Birmingham on Friday, started on the bench before replacing Alan Browne in the 67th minute.
Neil said the decision to start Sean Maguire instead of Hugill was purely a fitness one and not influenced by the transfer talk.
"Basically Jordan hasn't had the 90 minutes in his legs," said Neil.
"I think in the pre-season matches the most we got out of him was 70 minutes and he had a niggle when meant he didn't train for about a week-and-a-half.
"Sean Maguire was 17 games into his season and he is sharp as a tack at the moment, so it was a pretty simple decision."
Neil hopes Hugill will stay and says new signing Stephy Mavididi has not arrived as a replacement.
He said: "If you look at interest, Birmingham are interested in Jordan and they lost today and we won.
"Sometimes it is not just the fact someone is interested means someone will leave, we have a lot of positive things happening at this club.
"I think we can do well this year and I'm hoping Jordan and the rest of the squad are going to be part of that.
"Stephy is not a replacement for anyone."