The Honduran international has found the net only three times in his three-year Latics career but the importance of his latest strike could not be underestimated.
His side appeared to have been frustrated in their bid for victory despite throwing everything at the visitors in the latter stages of the second half after Tom Cleverley had equalised Liam Ridgewell's disputed opener in the 25th minute.
But when the impressive Cleverley rolled the ball back from the byline in the second of five minutes of added time the left-back switched it on to his weaker right foot before smashing a shot past goalkeeper Ben Foster.
Figueroa has history for dramatic interventions, with his previous goal being the 60-yard effort at Stoke last season.
Whether this latest effort will be enough to keep Wigan in the top flight remains to be seen but it lifted the bottom side to within two points of safety.
More importantly, only a second league win in 12 games will boost confidence for the remaining eight matches.
It also sucked Carling Cup winners Birmingham further into the dogfight as they slipped to second bottom, just a point above the Roberto Martinez's side.
More often than not the Latics have been their own worst enemies but they certainly had cause for complaint when the visitors took the lead after just six minutes.
Martin Jiranek's flick-on appeared to catch three Birmingham players in an offside position on the edge of the Wigan penalty area but with no flag raised Ridgewell reacted quickest to shoot past Ali Al Habsi.
It was Jiranek's last significant involvement as he was replaced by Curtis Davies because of injury soon after.
The substitute's first touch almost created a second goal when he headed Sebastian Larsson's corner back across the six-yard area where Cameron Jerome's shot on the turn was well blocked by Al Habsi.
Apart from Cleverley's early shot the hosts had not threatened but out of the blue the on-loan Manchester United midfielder equalised in the 25th minute.
Ben Watson's brilliant through-ball inside left-back Ridgewell picked out over-lapping right-back Emmerson Boyce and Foster could only push his cross into the path of Cleverley who gratefully accepted the gift inside the six-yard box.
Wigan nerves were not completely banished though and Figueroa, who had a shaky first half, gave the ball away to Jordon Mutch but fortunately for the Honduras international the midfielder's 25-yard shot was well off target.
Late in the half Charles N'Zogbia deflected over Boyce's cross from close range while Larsson hit the crossbar with a free-kick.
As expected the game opened up after the break, with Craig Gardner breaking clear of the defence but shooting straight at Al Habsi.
At the other end N'Zogbia's trickery allowed him to find space in the area but Cleverley swung wildly at his cut-back and Foster saved well as Figueroa blasted the loose ball at him from eight yards.
With time - and matches - running out Martinez made a double attacking change by sending on Hugo Rodallega and Conor Sammon for Franco Di Santo and Victor Moses.
Birmingham did likewise as, having replaced the ineffective Jean Beausejour with David Bentley, they sent on Obafemi Martins for Mutch as Alex McLeish also went in search of victory.
Sammon's flicked header from Cleverley's cross was claimed comfortably by Foster before Antolin Alcaraz and Davies were both booked as tackling became more desperate.
The introduction of the two substitutes had injected new life into Wigan and Sammon and McCarthy both had shots charged down in the area as the home side, for the first time in the game, looked like being the ones most capable of scoring.
With 10 minutes remaining Rodallega had the ball in the net after looping a shot over Foster but referee Lee Probert ruled the Colombia international had pushed Johnson as they challenged on the edge of the area.
McCarthy then wastefully blazed over after the impressive Cleverley had teed him up 20 yards out.
Foster had to scramble to turn aside a late deflected N'Zogbia strike but the England international was stunned when a late shot from Figueroa whistled past him in the 92nd minute.