Wiseman, who on Tuesday made his debut for Gibraltar in the country’s first game as a full UEFA member against Slovakia, headed Liam Feeney’s cross into his own net with 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 which extends the gap between the two sides to six points.
Reds boss David Flitcroft said: “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.”