The Australian struck four minutes into injury time after Blackpool substitute Matt Phillips thought he had earned a point with an 85th-minute equaliser at Bloomfield Road.
Blackburn had led since the 20th minute of the Premier League encounter when the otherwise excellent Charlie Adam inexplicably headed into his own net.
It was only Blackburn's second win of the season and brought relief to their manager Sam Allardyce - sacked by Blackpool 14 years ago - after squandering leads in four previous games.
Defeat was harsh on the Seasiders in their first league meeting with their neighbours for 30 years.
They started and finished strongly and Adam went close to making amends for his blunder three times.
Goalkeepers Matthew Gilks and Paul Robinson both had fine individual games in a match characterised by free-flowing attack, and both sides hit the woodwork.
It was Blackpool who made the better start.
After his defensive tactics at Chelsea backfired last week, manager Ian Holloway gave his players licence to get forward.
Brett Ormerod and Marlon Harewood returned in a three-man front line with DJ Campbell and the Seasiders' intentions were immediately clear as they went close to claiming a second-minute lead.
Gary Taylor-Fletcher first raced through to reach a Neal Eardley cross but saw his volley deflected wide.
The hosts then hit the woodwork from the resulting corner as David Vaughan's cross was met by a firm Ormerod header.
His effort was on target but Michel Salgado managed to get his head in the way and the ball ricocheted onto the crossbar before being cleared.
Blackpool threatened again when Ormerod delivered a dangerous cross but Gael Givet put the ball behind for a corner and Vaughan then curled a shot narrowly wide.
Blackpool's good early work was undone after 20 minutes as Adam, one of the stars of last season's promotion campaign, had a complete aberration.
The Scotland international was under no pressure as a Blackburn attack began to fizzle out.
Nikola Kalinic's flick-on posed no danger as it fell to Adam six yards out but his attempt to cushion a header back to Gilks completely wrongfooted the goalkeeper.
The ball bounced into the centre of the net and Blackburn, having started to retreat, celebrated an unexpected gift.
Rovers were then inches away from a second six minutes later as Christopher Samba met a Morten Gamst Pedersen free-kick with a deft header against the post.
Blackpool struggled to clear but escaped further damage as Kalinic blasted wide after a goalmouth scramble.
Adam had a chance to redeem himself with a 25-yard free-kick after Taylor-Fletcher was checked in full flow, but the wall blocked his powerful drive.
Kalinic had another good chance before the break but struck the side-netting after being teed up on the edge of the area by Pedersen.
Blackpool were fortunate not to concede again early in the second half as El-Hadji Diouf began to terrorise Eardley down the left.
The former Liverpool forward cut the hosts open before setting up Emerton inside the box, but Gilks parried his drive.Diouf was given chance to cross again but Kalinic's elaborate attempt at a volley flew wide.
Diouf whipped in another cross soon after and Gilks produced an even better save to keep out a Phil Jones header from point-blank range.
Jones blocked an Ormerod shot at the other end and the veteran Blackpool striker then hit the side-netting after good work by the tenacious Vaughan and Campbell.
Kalinic endured more misfortune when he headed over the crossbar and Adam went close at the other end with a back-post header that drifted across the face of goal. Eardley almost turned it in but agonisingly failed to get a touch.
Blackpool turned up the heat and Taylor-Fletcher forced a brilliant save from Robinson with a shot curling into the corner.
Robinson was then needed again to palm over an effort from Adam which took a wicked deflection.
Pressure finally paid off as Holloway made an inspired substitution by replacing Eardley with Phillips.
Phillips had barely been on the field a minute when he jinked his way into the box, beat Givet and found the bottom corner.
Blackpool thought they had claimed a point but Blackburn had other ideas and snatched victory when a Benjani Mwaruwari shot was blocked and Emerton stabbed home.
Source: PA