Pompey were undone by two second-half goals at the Wellington Sports Ground.
Keolan Lavery struck on 63 minutes before adding a second late on to seal victory for the Tractor Boys.
Director of youth operations Paul Smalley said: “We produced good performances all over the pitch but a disappointing end to the game saw us concede twice against the run of play.
“Their goals came about because of two lapses of concentration by us.
“But even when we were two goals down we fought hard and created chances. Some of our players were also returning from injury.
“There are plenty of positives to take – we defended well and attacked creatively but just lacked that clinical edge.
“And we’re still on track in our mission to see the players progress and improve.”
Pompey: Fry; Tallack, Bennett, Grant, Butler; Stockford (c) (Colson 77), Higgins (Tsovolos 55); Wheeler, Harris, Cook (Vine 55); Walshe
Subs not used: Fitzharris, Seeley
Ipswich: Chopper; Bennett, McKeoun, Munhako (October 27), Whight; Scotchor, Jones; Winter (Marriott 63), Carson, Trofak; Lavery
Subs not used: Oddonneil, Lawrence, Acott
There was better news for Pompey’s under-16 side who beat Ipswich 2-1.