Palace, who lost 4-1 at Portman Road in the Coca-Cola Cup, reacted furiously when David Tuttle was penalised for handball as Paul Mason flicked the ball up against his arm.
After Andy Roberts had been booked for dissent, Adam Tanner drilled his rising shot to Chris Day's right to give Ipswich a deserved lead and they increased it in the 52nd minute when Mason collected a throw from Mauricio Taricco and unleashed a spectacular 30-yard right-foot effort for his 10th goal of the season.
However, in the 65th minute Palace replied with a penalty from Dean Gordon after Jason Cundy had tripped Neil Shipperley.
Suitably inspired, Palace surged forward in search of an equaliser and Gus Uhlenbeek cleared off the Ipswich line from Carl Veart. Then, in the 77th minute, a misplaced backheader by Tanner let in Shipperley, who rolled his shot just wide.
Two minutes later, though, Palace were caught out when Geraint Williams had an effort blocked and Richard Naylor drilled in the third Ipswich goal from the edge of the penalty area.
Ipswich Town: Wright; Stockwell (Dyer, 86), Taricco, Cundy, Sedgley (Tanner, 24), Williams, Uhlenbeek, Sonner, Naylor, Scowcroft, Mason. Substitute not used: Forrest.
Crystal Palace: Day; Edworthy (Hopkin, 60), Gordon, Roberts, Tuttle, Quinn (McKenzie, 86), Muscat, Ndah, Shipperley, Dyer (Freedman, 60), Veart.
Referee: G Singh (Wolverhampton).