Paul McGuinness' side were on top for long periods but had no real cutting edge and were undone by two goals against the run of play. George Colson drilled the opener into the corner of Liam Jacob's net and the Australian keeper was beaten by Alexander Grant to a dangerous free-kick for the eventual winner.
The young Reds looked a little rusty with their finishing as Jack Rudge, Mats Daehli and Joe Rothwell were all off target in the first half and Matt Gledhill saved well from Daehli and Jack Barmby.
After the break, Tom Lawrence had a goal rightly disallowed for a push following a neat move and another promising build-up led to Barmby firing straight at Gledhill. Injuries to players from both sides, including United's Matthew Wilkinson, disrupted the flow of the second half and the Reds were grateful to Jacob for keeping out Adam Webster's point-blank header and to see Ashley Harris' effort ruled out for offside.
It allowed Lawrence to give his side hope when steering home after great approach work from Daehli and Rothwell but Pompey held out with Tyler Blackett booked late on for dissent as frustration started to grow.
United: Jacob; Hendrie, Wilkinson (Weir 67), McCullough, Blackett; van Velzen, Rudge, Rothwell, Daehli; Lawrence, Barmby. Subs not used: Pearson, Coll, Gorre.