Three vital points at the DW Stadium saw Latics climb up to 12th in the Championship, but they were made to work for it, coming from behind with second half substitute Emmerson Boyce scoring a stoppage time header to dramatically seal the win.
Latics fell behind early on to a Tommy Spurr goal, but Blackburn faced 59 minutes of the game with ten men after Grant Hanley struck Nick Powell with a raised arm.
Substitutes combined to complete a memorable come back as Grant Holt on his return from injury forced Spurr to put the ball into his own net, before Boyce's injury time winner.
Owen Coyle made two changes from the team that beat NK Maribor 3-1 in the Europa League on Thursday as James McClean and Thomas Rogne returned to the side in place of Callum McManaman and Emmerson Boyce.
It was a cagey start to the afternoon, with both sides struggling to put a foot on the ball in the first five minutes as control of the game couldn't be determind.
Eight minutes in though there were no complaints from Blackburn on that matter as they took the lead through defender Tommy Spurr.
A foul by Ryan Shotton allowed Tom Cairney to launch a high ball into the area and with Leon Best challenging Scott Carson, the goalkeeper couldn't hold onto the ball as it bounced out to Spurr inside the area who composed himself and struck the ball in off James McArthur.
As Carson jumped with Best there seemed to by an infringement from the former Newcastle United man, but referee Stuart Attwell allowed the goal to stand.
Latics' first chance came 15 minutes in after a simple but effective passage of play by Ben Watson, James McClean and Jean Beausejour allowed McArthur to push the ball out of his feet on the edge of the area and strike just wide of the right post.
Watson found McClean wide right, the winger cut across the pitch to find Beausejour on the opposite flank and shaping to cross left footed, he checked back to find McArthur.
Although controversy could have been claimed for the Blackburn goal, it was plain and simple for the next big decision of the game as Grant Hanley was given his marching order when he struck Nick Powell in the back of the head with his fist.
Powell pressed and harried the defender and upon releasing the ball to a team mate, Hanley brought his arm up behind Powell head sending him to the floor and giving the referee no alternative but to send him off.
From then on in it was constant Latics pressure until half time, with plenty of crosses into the box, but some solid goalkeeping from Jake Kean who was time and time again off his line to punch clear.
The second half had one theme written all over it, attack versus defence with the occasional break from the away side.
After early second half pressure and few chances, little did anyone know how significant a 62nd minute substitution of Emmerson Boyce for Ryan Shotton would be.
Grant Holt was also brought on to add presence up front and it paid off with excellent consequences as Latics finally took advantage of one of their plethora of corner kicks.
On 69 minutes Jordi Gomez provided the ball into the box and the bullish run and head of the ball from Holt ricochet back out off a Blackburn defender on the line, hitting Tommy Spurr facing the goal, leaving him with his head in his hands as he put the ball in the net for the second time during the afternoon.
More and more corners and crosses were went into the area from the likes of Watson, Beausejour, McClean and Gomez but Blackburn stood firm, despite some panic in the ranks, with Lee Williamson even having to over head kick clear.
Beausejour lashed a volley wide after he chested down a clearance, showing just how much Blackburn were defending as they limited Latics' points of attack.
McClean hit the side netting, Powell had a close range shot blocked and then the Republic of Ireland winger fired one behind at the back post from yet another Latics corner.
With a minute of normal time remaining Joshua King almost punished Latics when he cut in from the left wing to fire a rasping effort just inches over the cross bar with his right foot as the top of the netting rippled.
Moments later the fourth official signalled for a minimum of five minutes added time, but Latics needed just one of those to score a last gasp winning goal.
Jordan Rhodes was the culprit to concede a free kick just inside his own half as he wiped out Gomez in an aerial collision.
Blackburn substitute Chris Taylor tangled with Powell in the box before the free kick was taken, delaying what was always going to be a nervy ball in the box for the away side's defence.
In it came from Watson, up went Boyce and in went the ball as the defender turned his header in off the back post, sending the DW Stadium into a frenzy and sparking wild celebrations on the pitch.
Latics held out for the three points will relative ease as Blackburn mistakes saw them unable to mount any sign of a late equaliser.