Dave Beasant saved a second half penalty for ten-man Albion against his former club, but it was not enough to rescue the Seagulls from a damaging defeat.
Steve Coppell's men were already 2-1 down and down to ten men when the veteran keeper marked his first home appearance by stopping Neil Shipperley's 54th minute spot kick.
An eventful match turned on a red card for the recalled Gary Hart on 45 minutes after a tussle off the ball with Norwegian defender Trond Andersen.
Paul Brooker had given Albion a flying start with his third goal of the season after three minutes.
David Connolly headed Wimbledon level on 39 minutes and an electric finish by new signing Moritz Volz put the visitors ahead against the ten men on 48 minutes.
Republic of Ireland hitman Connolly put the issue beyond doubt on 79 minutes with his 16th goal in 14 League games.
Bobby Zamora scored an 86th minute consolation, but Albion are now staring relegation in the face.
Albion made a couple of changes to the team which suffered an unfortunate 1-0 defeat at Walsall on Saturday.
Rodger came in for his first start since Boxing Day in place of the injured Richard Carpenter.
Barrett paid the price for his goal famine, Hart taking over upfront for his first start since December 7.
Wimbledon, wobbling more than wombling of late, welcomed back star striker Connolly from a hamstring injury following Saturday's 3-2 home defeat against Nottingham Forest.
German youth international defender Volz made his debut for the Dons on a month's loan from Arsenal.
Sompting-based boss Stuart Murdoch also recalled Andersen for the injured Mark Williams.
Albion, having fallen behind after only seven minutes at Walsall, got the early goal themselves this time.
Zamora, latching on to Paul Watson's pass over the Wimbledon defence, had a shot blocked into the side netting by Leigertwood.
Rodger's resulting corner seemed harmless enough, but Kelvin Davis made a mess of it. Diving full length, the Dons' keeper could only parry the ball into the path of Brooker, who slotted his first goal at home this season from 12 yards.
Wimbledon were almost level three minutes later as Connolly toe-poked inches wide from close range.
Albion continued to look bright going forward, Zamora almost doubling their advantage in the 18th minute. He got the better of Gier from Jones's long pass before swivelling to blaze over the bar with his normally deadly left foot.
Wimbledon's anxiety at the way the contest was developing was emphasised by a rash challenge by Francis on Jones, which earned the midfielder a booking.
The Seagulls nearly scored again from a Rodger corner midway through the half. It was nodded on by Mayo towards the near post just out of reach of the leaping Pethick at the far post.
Zamora's angled drive from ten yards flashed just wide of the far post moments later as Albion continued to carve out chances.
Ainsworth collected a caution for an over zealous tackle on Mayo which, ironically, left the Wimbledon player requiring treatment.
Wimbledon levelled out of the blue six minutes from the break as Albion fatally lost concentration at the back.
Ainsworth's penetrating cross from the right flank was headed firmly home by Connolly, escaping goal side of Pethick.
The Seagulls suffered a further blow just before half time, Hart receiving a straight red card from referee Joe Ross following an incident off the ball midway inside Wimbledon territory involving Andersen. An angry Hart and his team mates clearly felt the visiting defender had feigned injury.
An eventful opening 45 minutes ended with a 30 yard volley by Watson forcing Davis into a spectacular tip over his own bar.
The last thing Albion needed with their numerical disadvantage was to concede again early in the second half, but that is exactly what happened. Volz surged forward three minutes into the restart, exchanging passes with Francis before cracking a right foot drive past Beasant from 12 yards.
Coppell responded by switching to a flat back four, Blackwell replacing Watson with Pethick and Mayo switching to the fullback positions.
Pethick dipped a 35-yarder just over the bar before ref Ross incurred the wrath of the home fans once more by awarding Wimbledon a penalty for Cullip's challenge on Shipperley as the visiting skipper shaped to shoot.
Ross relied on his linesman before pointing to the spot. It was a case of deja vu for Cullip, who conceded a penalty in Albion's 1-0 defeat against Wimbledon at Selhurst Park in August.
Shipperley scored on that occasion,but this time his penalty was dramatically saved by his former Southampton and Nottingham Forest colleague Beasant as he dived to his right.
Oatway had his name taken for dissent, while Volz went into the book for a foul on Jones.
The Seagulls brought on Barrett for Brooker and Piercy for Jones but their fate was sealed by Connolly 11 minutes from time. He held off Cullip to slip his second of the game past Beasant from close range.
Pethick was booked for a foul on Darlington before Zamora grabbed a consolation with four minutes remaining as Barrett set him up.
Albion (5-2-1-2) Beasant (gk) 8; Watson (rwb) 6, Mayo (lbw) 7, Cullip (cd) 7, Hart (f) 5, Oatway (m) 7, Brooker (m) 7, Pethick (cd) 6, Jones (lwb) 6, Zamora (f) 7, Rodger (m) 7.
Subs: Blackwell for Watson (withdrawn 50), Barrett for Brooker (withdrawn 69), Piercy for Jones (withdrawn 76), Rogers, Packham.
Goalscorers: Brooker (3), Zamora (86).
Sending off: Hart (45).
Bookings: Oatway (59, dissent), Pethick (84, foul).
Wimbledon (4-4-2) Davis, Ainsworth, Francis, Shipperley, Connolly, Andersen, Volz, Leigertwood, Gier, Darlington, Re-Coker. Subs: Gray for Connolly (withdrawn 80), Hawkins, Agyemang, Nowland, Gore.
Goalscorers: Connolly (39, 79), Volz (48).
Bookings: Francis (19, foul), Ainsworth (32, foul), Volz (61, foul).
Half-Time Albion 1 Wimbledon 1.
Attendance: 6,111.
Fan's View: Mick Vincent (Brighton).
In a lot of ways this must have been the most depressing night of our season.
As the Palace Pier burned, it felt as if the Albion's chances of First Division survival were also going up in smoke.
A promising start with a goal from Brooker seemed to bode well but an appaling standard of refereeing played a major part in how the game evolved.
It is too easy to blame referees however but by the time he blew the final whistle the anger among the crowd had largely turned to disappointment and frustration with the team itself. Even Bobby's goal never looked like being anything more than a consolation.
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