Wiseman, who on Tuesday made his debut for Gibraltar in the country's first game as a full UEFA member against Slovakia, deflected Liam Feeney's cross with just 13 minutes remaining to keep the Tykes in the relegation zone.
The defender's error, however, 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.
"And 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."
The on-loan Stoke keeper, though, could do nothing to stop Wiseman's header late on, a goal which eased the pressure on Millwall boss 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.
"We've been trying to get a clean sheet. When you concede one you have a chance but when you concede two or three it's always difficult.
"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 with the win."
Guy Moussi made his Lions debut after signing on loan from Nottingham Forest in the week and Lomas believes the midfielder will have an impact in his time at the Den.
"I thought he did well on his debut for a guy that hasn't played much football and he's come back from a groin injury," he said.
"I thought he did really well to come through the 90 minutes. Guy will play an important part next week."
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