The Lilywhites were well off song in the first half as Ipswich scored the game's only goal through Mustapha Carayol and had other chances to extend their advantage.
After the interval when the visitors sat off to defend their lead, North End lacked the guile and creativity to break them down.
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PNE manager Neil said: "I don't think we played anywhere near the levels we can, it was flat and we never got going.
"Probably that was down to how much we have demanded of the players, how our games have ended-up panning out, we have had three really tough fixtures with Brentford, Wolves and Aston Villa.
"We took a lot out of ourselves in those three games, for two of them we played with 10 men for 20 minutes and then 35 minutes.
"The team largely has been unchanged because other lads are struggling - Paul Gallagher has had only one day's training, Daryl Horgan hasn't had a lot of game time recently, neither has Josh Harrop.
"We could have put them in but I just felt that the lads who have been performing very well for us and with the importance of the game, we wanted to see if they could do it again.
"Unfortunately even yesterday I sent them in early from training because they looked flat and tired - I thought that continued into today.
"I tried a few things to get them going, I was really dissatisfied at half-time as you could imagine.
"To be fair you could see the players were disappointed, they wanted too play well today but they didn't have the energy.
"I probably changed systems more today than I had ever done as a manager which to be honest that is not something I'm not overly comfortable with and don't do generally.
"I believe that if you set up a way of playing, you should be good enough to play that way and beat them.
"But it didn't think we were going to create anything, I had to do something to spark something into the team and if I'm being honest it didn't work."
Neil substituted Calum Woods and Callum Robinson in the 38th minute, replacing them with Harrop and Josh Earl.
Explaining the early double change, Neil said: "We got a warning with Carayol down that left hand side, he should have scored on two different occasions and I could see the goal coming.
"Calum Woods made an error for the goal and he didn't look he was up to the speed of the game really.
"Likewise with Callum Robinson at the top end of the pitch, he looked fatigued as well and a yard off things.
"I thought we needed some fresh blood in the team but being honest, it didn't make any difference."