It remains a winless 2018 for Pompey after James Bolton's close-range strike proved the only difference between the Blues and the Shrews in a bad-tempered affair at rainy Fratton.
He poked in a first half corner and Pompey, not at their best but showing plenty of effort in poor conditions, had no answer - though sub Brett Pitman twice came close to salvaging a point. They weren't helped at a very poor showing by referee David Coote.
Adam May was sent off for a second bookable offence in injury time to compound the Blues' midfield woes - and an extra body in that department seems to be a must for Kenny Jackett before Wednesday night's transfer deadline.
With Pitman on the bench and Oli Hawkins and Kal Naismith tried as a forward partnership, with Jamal Lowe wide left, while Gareth Evans and Adam May were back in the starting line-up.
The Blues had the better of the first half possession but found themselves a goal down at the break.
Oli Hawkins almost connected with a couple of decent balls into the box from the right, where Evans was causing probems for Paul Hurst's side.
How Pompey were not awarded a penalty for Shaun Whalley's clear handball that helped the Shrews clear a Jamal Lowe cross only ref Coote will know. He also missed a fairly obvious shirt-tugging foul on Christian Burgess at a corner.
Shrewsbury's goal was a rather soft one from a Pompey viewpoint. A corner eluded everyone and was not cleared and Bolton scored from close range among a sea of bodies.
Evans and Hawkins threatened again as the half came to an end with the crowd getting angry not only at the officials but also at some poor tactics by some of the visiting players.
Pitman replaced Lowe 10 minutes after the break and immediately pepped up Pompey.
Soon the leading scorer's top-corner-bound header was superbly clawed away by keeper Craig MacGillivray - who again kept the Shrews lead intact when Naismith let fly with a goalbound effort from 25 yards or so.
Connor Ronan came on with 20 minutes left and his header set up Pitman for a shot that rattled the bar with six minutes left.
May saw red for a second booking as he hauled down Stefan Payne on a Shrewsbury counter attack - he is likely to miss only one game - while at the other end Pitman connected with a high cross to the far post but his effort flew low across the goalmouth and out for a goal kick.
The defeat leaves Pompey still ninth and still only five points off the top six - but with the mid-table pack closing in behind them.
Doncaster are next up, at Fratton next Saturday.
Pompey: McGee; Thompson, Burgess, Clarke, Donohue; May, Close; Evans, Naismith (Ronan 70), Lowe (Pitman 55); Hawkins. Subs not used: Bass, Deslandes, Bennett, Kennedy, Chaplin
Referee: David Coote
Attendance: 17,779 (498 away fans)
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