The Premier League Cup group F encounter appeared to be heading for a stalemate, a fair outcome in an instantly-forgettable match lacking quality.
Both reserve teams struggled to impress, with goal-scoring opportunities few and far between – until the final minute.
With a corner delivered from the right, Jacob Brown rose highest to plant a firm header past Alex Bass and clinch a 1-0 victory for the visitors.
It was decisive, settling a poor encounter involving a youthful Blues line up.
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With Kenny Jackett focusing on Saturday’s Checkatrade Trophy fixture with Northampton, Drew Talbot represented the sole senior player.
Others in a fresh-faced side included Alex Bass, Adam May and Joe Hancott.
Meanwhile, the Tykes fielded Victor Adeboyejo, a striker who trialled with Pompey earlier this season, impressing Jackett before making the switch to south Yorkshire.
And it was the visitors who took victory at the death, leaving the Blues still searching for their first group win.
During a tight opening, it took 21 minutes for Pompey to create their first opportunity, with Theo Widdrington swivelling from eight yards out to sweep a shot well over the bar.
Yet it proved to be a half bereft of clear-cut chances for either side in an uneventful period of play which offered little to the cold crowd.
There was a flurry of activity just before the interval when Dan Smith angled shot from the left was saved low down by Jack Walton, then Leon Maloney spun to strike a shot straight at the keeper.
However, both sides entered the interval goalless and in need of a breakthrough.
Minutes after the restart, Adeboyejo received the game’s first booking for simulation, after tumbling to the floor inside the penalty area.
Bradley Lethbridge was introduced for Maloney on 56 minutes, yet seconds later, at the other end, Brown blazed the ball out of the ground with a first-time shot inside the box.
On 70 minutes, a misjudgement of the bounce left Pompey with three men clear on the counter, however, the Barnsley keeper rushed off his line to superbly tackle Smith and the danger was cleared.
Then, on 90 minutes, Brown rose to settle a poor encounter.
Pompey: Bass, Talbot, Dandy, Casey, Hancott, Smith, Bedford, Maloney (56 mins Lethbridge), Widdrington, May, Mayes (83 mins Johnston).
Subs Not Used: Pitman, Read, Brooks.
Barnsley: Walton, Smith, Williams, Bird (79 mins Dolan), Fielding, Lund, Wardle, Wolfe, Brown, Adeboyejo, Palmer.
Subs Not Used: Ocran, Tingle, Miller, Swinburn.