Barnsley travelled to The New Den boosted by the knowledge they beat Millwall twice last season.
And the Reds took on the Lions in East London looking to extend a welcome four-game unbeaten run after a tough start to their Championship season.
The loss of leading scorer Chris O’Grady ahead of the match due to injury was unwelcome, but Reds’ boss Flitcroft employed playmaker Paddy McCourt behind lone striker Pedersen as the visitors went in search of goals on their travels.
But there was just one chance in the opening 20 minutes – and that went the way of the hosts.
Winger Waghorn weaved his way in from the wide flank, but his lack-lustre left-foot shot flew harmlessly wide of keeper Butland’s left-hand post.
Holding midfielder Moussi latched on to a loose ball as the Reds failed to clear their lines in the 28th minute, but the Frenchman saw his long-range left-foot shot charged down.
The Reds broke on the counter-attack and Pedersen shot straight at keeper Forde when he might have been better place to spread the play left to the unmarked Mellis.
Waghorn struck a crisp free-kick straight at Butland on the half hour ark after defender M’voto had conceded a careless foul on the edge of his own penalty area.
And a minute later winger Woolford combined well with striker McDonald, only to see his right-foot shot blocked on the edge of the box.
Pedersen teed up Mellis moments later after some smart work from the Reds, but the latter saw his low shot saved by Forde with his legs.
Five minutes before the break Moussi tried his luck from distance, but he miscued horribly and his shot was a long way off the target.
Midfielder Bailey also tried his luck from distance soon after, but he blazed well over much to the frustration for the home side.
The Reds started brightly at the start of the second half and could have been in front after just 33 seconds.
O’Brien dashed down the right and his cross picked out Mellis at the back post, but the midfielder was unfortunate to see his goal-bound head deflect off right-back Hoyte and out for a corner. No deflection and it could have been the opening goal of the game.
McCourt found himself the first player to be booked after he hauled down Malone, who had beaten him for pace as the home team countered.
Then Millwall made their first change of the afternoon with Feeney introduced in place of Chaplow to add an additional attacking threat.
Lions’ boss Lomas introduced a second sub soon after with Morison brought on to replace McDonald.
But the Reds defence held firm and some timely last-ditch tackles from Cranie and M’voto only added to the East London side’s frustrations.
Right-back Wiseman, who made his senior international debut for Gibraltar on Tuesday, then missed a glorious chance to put the visitors ahead.
Malone failed to clear Kennedy’s left-wing cross and Wiseman pinched the ball, only to poke agonisingly wide of the left upright.
Flitcroft then replaced Pedersen with fellow striker Scotland, presumably hoping fresh legs up front would yield a different reward. And just moments later striker Dagnall came on for Mellis as the Reds continued to look to make a breakthrough.
McCourt had a shot charged down on the edge of the box in the 72nd minute, but the Reds nearly went behind but for a wonderful save from Stoke City loan keeper Butland.
The England Under-21 international spread himself brilliantly to block substitute Lomas’ close-range shot at the back post.
But the Reds did concede less than a minute later with after a bizarre own-goal from WISEMAN.
Sub Feeney’s right-wing cross was headed into his own net by Wiseman as he attempted to clear the ball. It was a cruel blow for the Reds.
Scotland turned his marker with seven minutes left and fizzed a powerful right-foot effort just wide of Forde’s left post.
The Reds battled hard to get an equaliser but were made to count the cost for earlier missed chances – and their four-game unbeaten run came to an end. Victory for Millwall was their first for seven games.