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.
Scott McDonald was involved in both early openings for the hosts. The striker - with three league goals this season - cut in from the right and shot wide, before teeing up Martyn Woolford whose cross-shot was well parried by Jack Butland.
An unmarked McDonald then scuffed Richard Chaplow's cross in front of goal with just Butland to beat, and after debutant Guy Moussi saw his follow-up blocked, Barnsley were able to break.
However, Marcus Pedersen failed to play an easy ball to the left which would have set Jacob Mellis through on goal, instead trying his luck from 25 yards which was an easy save for David Forde.
That combination almost brought a reward later in the half as Norwegian international Pedersen played a lovely first-time pass to Mellis, but the midfielder could not beat Forde.
Nicky Bailey tried his luck on the stroke of half-time, but his long-distance strike failed to trouble Butland, who enjoyed a fairly quiet half.
Mellis nearly gave Barnsley an ideal start to the second period but his header at the back post was deflected wide for a corner.
Millwall, who played in their white away kit in support of Prostate Cancer UK, began to press more but struggled to create any openings against a Barnsley defence that kept their first clean sheet of the Championship season at home to Doncaster in their last match.
With the home crowd finding its voice, the match finally opened up although neither side offered much in the final third.
Barnsley were nearly gifted the lead when Millwall defender Scott Malone chested down Tom Kennedy's cross towards his own goalkeeper, only for Wiseman to nip in - fortunately for Malone, Forde got the block in to divert the ball wide.
Steve Morison came on for Millwall while Barnsley manager David Flitcroft threw on Jason Scotland and Chris Dagnall as both sides pressed for the decisive goal.
Morison came close to scoring, but from a low left-wing cross his shot was brilliantly saved by Butland, on-loan from Stoke, when it looked like a goal was certain.
But minutes later, substitute Liam Feeney's cross was headed into his own net by Wiseman to give Millwall the lead.
Try as they might, Barnsley failed to grab an equaliser that confirms their worst start to a league season since 1973.