Barnsley equalled an unwanted club record by going 11 home matches without a win, a record they set in 2012-2013.
On the flip side Millwall also equalled one of their club records by securing a sixth successive away win.
This result ended Barnsley's five league match winning run against the Lions.
Millwall knocked Barnsley out of the FA Cup with a 4-1 win at the Den in January meaning they have won back to back games against the Reds for the first time since 1993-1994.
This was Millwall's first win at Oakwell since January 2012 and only their second league victory in nine visits.
It is also the first time since that 2012 encounter that Millwall have scored more than once at Oakwell and only the third time in 11 visits.
Barnsley conceded the first goal for the 22nd time in 35 Championship games this season, the most since the relegation season of 2013-2014 when they conceded the first goal on 27 occasions.
Barnsley were behind at half time for the 14th time in the Championship this season, the most time they have been behind at the break since 2014-2015 (17)
Once again there was a half time substitution for Barnsley, George Moncur becoming 19th half time change this season!
Barnsley have now played 42 home league games since winning promotion back to the Championship, and won only nine. (W9 D18 L15)
Jose Morais has now lost four of his first seven league games in charge, the first Reds boss to do this since Viv Anderson in 1993 (Morais W1 D2 L4, Anderson W2 D1 L4)
Only Fulham (16 matches) are on a longer unbeaten run in the Championship currently than Millwall (12).
The Tykes have used the joint-most players in the Championship this season (34, level with Sunderland), while Millwall have used the fewest (24).
Barnsley have now only scored more than once in a match on two occasions in 25 outings, both coming against Birmingham.
Nick Townsend was back in goal as Adam Davies' partner was due to give birth, Barnsley have won only three of the 17 league games in which Townsend has featured.
Lee Gregory scored Millwall's first goal at Oakwell, meaning he has scored in both league meetings this season, the second opposition player to do this v Barnsley in 2017-2018, after Cardiff's Callum Paterson.
It is the second season in a row in which the two sides have met that a player has scored in both meetings, Sam Winnall achieving this feat for Barnsley in 2015-2016.
Referee Peter Bankes did not show a single card in the match - the first time in 32 matches (all comps) that there has not been a card shown in a Barnsley match, the last occasion was the FA Cup tie at Wembley against Tottenham in September.
It is the first Barnsley league match without a card since the 10th December 2016, in the 2-1 win over Norwich.
Despite defeat Barnsley had 64% possession, their most in a game this season, and the most since the final home game of last season against Burton (66%)
George Moncur (for Mallan 45)
Tom Bradshaw (for Potts 66)
Lloyd Isgrove (for Lindsay 81)
Jack Walton, Dimitri Cavare, Matty Pearson, Connor Mahoney.
Jordan Archer, Mahlon Romeo, Shaun Hutchinson, Jake Cooper, James Meredith, Jed Wallace, Shaun Williams, George Saville, Ben Marshall, Steve Morison, Lee Gregory.
Jason Shackell (for Gregory 75)
Fred Onyedinma (for Marshall 79)
Tim Cahill (for Morison 90)
David Martin, Ryan Tunnicliffe, Tom Elliott, Aiden O'Brien.
Millwall manager Neil Harris said:
"Any three points at this level is a good achievement.
"If you look at Barnsley, they have a distinct style of play - they've definitely improved. I thought we found another way to win the game, we dominated early on and then capitalised on a mistake.
"It was good composure from us to get the goal. I never felt in danger in the first half. We scored at a key time, Ben Marshall's goal was outstanding.
"I thought Barnsley threw caution to the wind in the last half an hour and were unlucky not to score."
Sky Bet Championship results:
Saturday 17th March 2018:
Fulham 2-2 Queens Park Rangers
Cairney 32 Luongo 45+3, Wszolek 81
BARNSLEY 0-2 Millwall
Gregory 24, Marshall 63
Birmingham City 3-0 Hull City
Brentford 1-1 Middlesbrough
MacLeod 34 Traore 21
Bristol City 1-0 Ipswich Town
Leeds United 1-2 Sheffield Wednesday
Grot 86 Nuhiu 71, 90+1
Norwich City 3-2 Reading
Vrancic 14 Kelly 32, Smith 51
Maddison pen 37
Sheffield United 0-0 Nottingham Forest
Sunderland 0-2 Preston North End
Maguire 50, Robinson 63
Wolverhampton Wanderers 3-1 Burton Albion
Costa 15 Dyer 44
Afobe 41, 56
Bolton Wanderers 1-0 Aston Villa
Le Fondre 19
Barnsley lie in 21st place in the Sky Bet Championship with 33 points from 38 games.
We are 29 points outside the Play-Offs, 43 points off the Automatic Promotion Places, 49 points off First place and Goal Difference above the Relegation Zone.
Up to 18/03/18
Sky Bet Championship Matchday Thirty Nine: Barnsley v Bristol City, Friday 30th March 2018. Kick-Off: 3pm
On The Road:
Sky Bet Championship Matchday Thirty Forty: Nottingham Forest v Barnsley: Monday 2nd April 2018. Kick-Off: 3pm