Richard Naylor saw red early on for his foul on Brett Ormerod, but Town took the lead through Jason De Vos' header.
However, Nugent hit two in nine minutes to put North End in front, firstly driving home Ormerod's lay-back and then stabbing home from close range.
And Patrick Agyemang ensured they moved back into sixth spot with a solo goal.
Ipswich manager Joe Royle:
"Referee Ilderton has agreed to look at the video again and I don't know if I'm hopeful or not. "It shows Brett Ormerod mis-controls the ball and is on his way to the floor before Naylor got near him.
"I'm also disappointed with the attitude of the Preston players, harassing to get him sent off."
Preston: Nash, Mears, Mawene, Davis, Hill, Sedgwick, Jarrett (Whaley 58), McKenna, Davidson, Ormerod (Agyemang 66), Nugent (Dichio 68).
Subs Not Used: Alexander, Lewis Neal.
Booked: Mawene.
Goals: Nugent 53, 62, Agyemang 71.
Ipswich: Supple, Wilnis, De Vos, Naylor, Barron, Currie (Sito 14), Juan (Westlake 27), Garvan, Richards, Fuller (Haynes 56), Lee.
Subs Not Used: Magilton, Price.
Sent Off: Naylor (11).
Booked: Haynes, Barron.
Goals: De Vos 38.
Att: 14,507
Ref: E Ilderton (Tyne & Wear).