Hugill, scorer of two goals last week at Aston Villa, netted in the 89th minute from a deflected Daryl Horgan cross.
It came against the club who had bid Â£1.5m and Â£2m for him in recent weeks.
North End had trailed from the 16th minute, Tom Lawrence's superb finish a rare piece of quality in a poor game.
He cut inside from the wing and fired into the far corner, leaving PNE to chase the game.
The hosts saw plenty of the ball but it was only in the latter stages that they started to cause chinks in Ipswich's armour.
Time was running out for North End when Hugill struck, that his ninth goal of the season.
Ben Pearson returning after a two-game suspension in place of Alan Browne had been the one change to the North End starting XI.
In the second minute, Daniel Johnson fired over the bar from outside the box after a Paul Gallagher corner had been cleared by the Ipswich defence.
Another early chance saw Aiden McGeady find Jordan Hugill with a cross from the box, Hugill unable to keep his header down.
Ipswich took the lead in the 16th minute, Lawrence coming inside off the left-wing past Marnick Vermijl before producing a superb right-foot finish into the far corner of the net.
Freddie Sears forced a routine save out of Chris Maxwell after getting down the right hand side of the box.
North End saw plenty of the ball as the first half went on but were in the main limited to shooting from outside the box.
McGeady, who carried their main attacking threat from the left-wing, saw two efforts disappear over the bar.
It was McGeady who produced a good chance in the 42nd minute, his cross from the left met on the volley from Pearson, the shot hitting team-mate Hugill and going wide.
Just before that at the other end, Ipswich had gone close to a second goal, Sears out-muscling Vermijl and getting a shot away which hit Maxwell on the leg and went behind.
As the interval appoached, Gallagher led a Preston counter-attack but his shot at the end of a strong run sailed over the bar.
Five minutes into the second half. Gallagher's goal was chested down by Callum Robinson but his shot lacked power and went through to the keeper.
Horgan joined the action from the bench in place of Robinson as North End looked for a way through a packed Ipswich defence.
Brett Pitman put a couple of shots too high for the visitors but in the main it was the home side on the attack, although they found it difficult making too much headway.
North End had two good chances inside the space of 90 seconds, the first a 74th minute shot from McGeady which keeper Bartosz Bialkowski dived to push away.
Soon after, McGeady stood up a cross to the far post which Tom Clarke met, the skipper's header deflected over the bar.
With Jermaine Beckford and Simon Makienok introduced in the later stages, Preston went to a 3-4-3 system and that was to pay off in the 89th minute.
Horgan's cross dropped over the Ipswich defence leaving Hugill with the space to turn and tuck a shot into the net from 10 yards.
PNE: Maxwell, Vermijl (Makienok 77), Clarke, Huntington, Spurr, Gallagher, (Beckford 65) Pearson, Johnson, McGeady, Robinson (Horgan 57), Hugill. Subs (not used): Browne, Boyle, May, Lindegaard.
Ipswich: Bialkowski, Emmanuel, Chambers, Berra, Knudsen, Lawrence, Skuse, Diagouraga (Bru 57), Ward, Pitman (McGoldrrick 73), Sears (Moore 79). Subs (not used): Bishop, Spence, Digby, Gerken.
Referee: Steve Martin (Staffordshire)
Attendance: 10,656 (346 away)