Wiseman, who had made his debut for Gibraltar in the country’s first game as a full UEFA member against Slovakia in midweek, deflected Liam Feeney’s cross with just 13 minutes remaining to keep the Tykes in the relegation zone.
The defender’s error secured the Lions’ first win in seven league games and extended the gap between the two sides to six points.
“He’s a team man, he’s a team player and he loves playing for Barnsley,” said Flitcroft of Wiseman.
“He’s absolutely devastated. He got his body position wrong and he’s paid the ultimate price for it.
“It’s a terrible goal to concede. He’s had some bad moments at the football club, but Scott will recover from that, no problem. That’s up to us on Monday to all get around Scott and make sure that he moves forward.
“On the balance of play, the game plan and what we tried to do, we deserved something, but we didn’t take opportunities to finish Millwall off and the game has probably hinged on that.
“It doesn’t surprise me that we scored the goal that won the game, but I’m disappointed that we’ve not come out of it with anything.
“I’ve got to draw the positives from the performance and I don’t think defensively we were shaky.”
Australian international striker Scott McDonald wasted a couple of good first-half chances for the hosts, but Jack Butland was equal to most of what the Lions could throw at him.
The on-loan Stoke goalkeeper, though, could do nothing to stop Wiseman’s header late on, a goal which eased the pressure on Millwall chief Steve Lomas.
“We’ve probably played better and lost,” said Lomas. “We had to dig in there and scrap and fight.
“When you’re not playing at your best you’ve got to work to get that clean sheet and hope something falls for you.
“We got a little bit of luck for the own goal, but I thought we deserved it and a clean sheet is something we’ve been striving for.
“Barnsley are on a decent little run themselves, so it was never going to be easy. They’re fighting for their lives so I’m delighted.”
Millwall: Forde, Hoyte, Robinson, Beevers, Malone, Bailey, Moussi, Waghorn (Easter 90), Chaplow (Feeney 56), Woolford, McDonald (Morison 61). Unused substitutes: Shittu, Martin, Smith, Bywater.
Barnsley: Butland, Wiseman, Cranie, Mvoto, Kennedy, O’Brien, Perkins, Etuhu (Dawson 80), McCourt, Mellis (Dagnall 70), Pedersen (Scotland 65). Unused substitutes: Hassell, Digby, Cywka, Dibble.
Referee: K Hill (Hertfordshire).
Man of the match: Jack Butland.