Albert Crusat appeared to have given Wigan the points in the 88th minute, but referee Andre Marriner awarded a spot-kick after David Jones fouled Rovers goalkeeper Paul Robinson, who was up for a late corner.
The goal was priceless for Blackburn's under-fire boss Steve Kean, who was barracked throughout by the massed ranks of Rovers fans before the sensational finale.
But the dramatic scenes were not witnessed by Rovers owners Venkatesh and Balajil Rao, who flew in from India this morning for the match but mysteriously left at half-time.
An extraordinary game also saw the 48th-minute sending-off of Blackburn midfielder David Dunn and a controversial second goal for Rovers in which Morten Gamst Pedersen appeared to take two touches from a corner.
Rovers, heading to the DW Stadium with Kean's future once again in the spotlight, had grabbed the lead after just 68 seconds when Yakubu lobbed goalkeeper Ali Al Habsi.
Wigan were level through Jordi Gomez seven minutes later and ahead through captain Gary Caldwell after 31 minutes, but Junior Hoilett equalised before a breathless finale in which either side could have claimed the points.
After eight straight Premier League losses, Roberto Martinez's Wigan started the game in desperate need of points but Kean also knew it was potentially critical to his future.
And a nervy game exploded into life in an instant with Yakubu pouncing on the end of a Steven Nzonzi header and lobbing the opener over Al Habsi with just 68 seconds on the clock.
Yakubu's strike must have delighted the Rovers owners but Martinez's men hit back with Victor Moses having a loud penalty appeal turned down.
But it took just seven minutes for the Latics to level when Grant Hanley's half-clearance fell to Gomez, who lashed a swinging left-foot shot home from the edge of the box.
Dunn and Ruben Rochina were both booked by referee Marriner in a manic first quarter of an hour in which both these struggling sides looked well up for battle.
The home side's committed play paid off again in the 31st minute when they grabbed the lead, Caldwell wriggling free of his marker to power home a header from a David Jones corner.
And Wigan should have gone further ahead in the 38th minute when Ronnie Stam found space on the left and delivered a cross which Moses blazed over the bar from eight yards.
With the home side well on top, discontent began to brew among the swelled ranks of Rovers supporters behind the goal, with some chants directed at the removal of Kean and the owners.
Jones looped a long-range effort just wide for Wigan at the start of the second half before Rovers were reduced to 10 men when Dunn received a second yellow card for hacking down Moses.
The Rovers owners missed their side's equaliser on the hour when a short corner deceived the Wigan defence and Pedersen crossed for Hoilett to prod in at point-blank range.
But there was controversy over the equaliser with replays appearing to clearly show Pedersen take two touches from the set-piece before delivering the ball in for the goal.
Rovers missed a great chance to reclaim the lead in the 72nd minute when Yakubu sprang clear and rounded Al Habsi before a brilliant saving challenge from Steve Gohouri.
Crusat, a replacement for Gomez after 68 minutes, brought a fine save out of Robinson from long range before the keeper stood firm to deny Rodallega from six yards.
Crusat then netted what appeared to be the winner in the 88th minute when Rodallega headed down and the striker prodded a low effort which deceived Robinson and bobbled into the net.
But there was still time for Yakubu to send Al Habsi the wrong way from the penalty spot to bring down the curtain on a remarkable DW Stadium clash.
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