Pompey's inconsistencies surfaced again as they let in two goals in the opening six minutes and left themselves too big a mountain to climb at Doncaster.
A freak own goal got them back in the contest early in the second half but Dion Donohue's needless red card halted their momentum and they failed to find an equaliser.
The result moves Pompey down to 11th in the table, a place below Saturday's hosts Blackburn.
Rovers were ahead in the fourth minute when Liam Mandeville converted from rodney Kongolo's square ball in. It got worse for Pompey a couple of minutes later when Christian Burgess made a hash of Harry Toffolo's corner and it went in past the helpless Luke McGee.
Pompey were shellshocked but did gradually improve, but it took a freak goal to get them back in it soon after the start of the second half.
Donny keeper Ian Lawlor passed along the deck to defender Mathieu Baudry and when the defender played the ball back, the keeper missed his clearance and could not scramble back in time to stop the ball crossing the line.
For a while Pompey looked good value to get something from the game but they were given a setback when Donohue was ordered off for stupidly kicking out at Rovers' Niall Mason.
Sub Jamal Lowe was so close to rescuing a point in the final minute of time added on but his glancing header from Matt Kennedy's cross was brilliantly kept out by Lawlor, making up for his earlier gaffe.
Pompey will now have to make sure they don't give another Rovers - Blackburn - anything like the head start they handed Doncaster, when they visit Ewood Park on Saturday.
Pompey: McGee; Thompson, Burgess, Clarke, Donohue; Close, O’Keefe; Evans (Lowe 46), Bennett (Chaplin 46), Kennedy; Hawkins. Subs not used: Bass, Haunstrup, Oxlade-Chamberlain, Rose, Naismith.
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