Blackburn dominated the first half, built a 2-0 lead and then were obliged to cling on desperately to their three points.
Former Southampton manager Souness saw his side overwhelm Pompey in the first half with some bright and attractive football, with goalkeeper Shaka Hislop needing to be at his best to deny Andy Cole and Tugay.
But it was no surprise when Blackburn took the lead in the 35th minute when full-back Lucas Neill shot home from 12 yards after a Cole effort had been hacked from the line.
It was a sweet moment for Neill who started the week under a cloud after being sent off in the home defeat by Liverpool for a leg-breaking tackle on Jamie Carragher.
Portsmouth were still reeling from that setback when Cole took a pass from Brett Emerton with his back to goal, swivelled past his marker and then beat Hislop with a powerful right-foot shot.
In first-half injury-time Teddy Sheringham, with five goals already this season, miskicked from six yards after being found in space by Tim Sherwood.
Portsmouth were a much improved side after the break and pulled a goal back in the 57th minute when Steve Stone took a corner on the right and defender Arjan De Zeeuw was unmarked when he headed home.
De Zeeuw hooked another good chance over the bar after 66 minutes and Sheringham flashed a header narrowly wide.
But there was a scare at the other end when Emerton smashed a fierce right-foot shot from 12 yards against the underside of the bar with the Portsmouth defence hopelessly beaten.
Harry Redknapp sent on big striker Vincent Pericard with six minutes remaining in a last-ditch attempt to snatch a draw, but Blackburn held on even with five minutes of injury time added on by referee Paul Durkin.
Portsmouth: Hislop, Schemmel, De Zeeuw, Stefanovic, Zivkovic, Stone, Sherwood, Faye, Quashie, Sheringham, Ayegbini. Subs: Wapenaar, Foxe, Pericard, Smertin, Roberts.
Blackburn: Friedel, Neill, Amoruso, Babbel, Gresko, Emerton, Tugay, Ferguson, Thompson, Cole, Jansen. Subs: Kelly, Johansson, Grabbi, Yorke, Baggio.
Referee: P Durkin (Dorset).