Blackpool missed a host of chances to condemn Portsmouth to a third straight defeat and, as a result, failed to move into the play-off positions.
Matt Phillips missed two clear-cut chances early on for the visitors whilst Jason Pearce was lucky not to concede a penalty for handball in an entertaining encounter at Fratton Park on Saturday that had looked set to finish goalless, until Huseklepp's late intervention - his first goal for Pompey.
The Tangerines dominated a tentative opening period, and had two glorious chances to go ahead in two minutes.
First Gary Taylor-Fletcher brilliantly picked out Matt Phillips after 15 minutes, and the former Wycombe man went around a defender but his instinctive shot was straight at Jamie Ashdown.
And the striker had another chance minutes later to put the visitors in front, this time dragging wide when well-found by strike partner Kevin Phillips.
Blackpool have not beaten Portsmouth in almost 38 years, but their quick counter-attacks and short passing were causing the home side a host of problems.
When Pompey finally found their stride Huseklepp's 25-yard effort flew just over Matt Gilks' crossbar, before Joel Ward lost his marker and headed the home side's best chance of the half wide from close range on the half-hour.
Steve Cotterill's men's task could have been made much more difficult when David Norris appeared lucky to escape a red card following an elbow on Ian Evatt.
The visitors, unbeaten away from home in the league this season, saw a stinging Tom Ince free-kick palmed over by Ashdown, before Barry Ferguson smashed a volley narrowly over just before the interval.
The home side came quickly out of the blocks in the second half with youngster Joel Ward's fine strike from 20 yards clearing the bar and Liam Lawrence forcing Gilks into a smart save after 50 minutes.
From the corner, Greg Halford stole in front of Alex Baptiste but his header flew just wide.
The game's most controversial moment came after 70 minutes when Evatt's goalbound shot seemed to strike the hand of Pearce, but referee Darren Deadman waved away the defender's furious appeals.
Portsmouth looked short of imagination up front without the suspended Luke Varney, with Benjani remaining largely anonymous.
Both managers made attacking substitutions as they bid for all three points, but it was Pompey who took them home when Evatt's mis-timed header fell to Norwegian striker Huseklepp, who hammered a volley home from 12 yards to leave Ian Holloway's charges reeling.
The winner came with less than a minute of stoppage time remaining and moves Portsmouth up five places to 14th as the Lancashire outfit drop to eighth.