This win made it eight wins out of 13 for caretaker boss Glenn Roeder to leave United in with a chance of a UEFA Cup place.
There was nothing unlucky about the win as a goal in each half took Shearer's seasonal tally to 13, with Titus Bramble notching his first of the campaign after Jimmy Bullard had given Wigan an early lead with a stunning free-kick.
Incredibly there were five first-half substitutions in the opening 42 minutes, three of them for Wigan.
Skipper Arjan De Zeeuw went off after 17 minutes with a suspected broken collarbone, following United's Shola Ameobi who broke two teeth.
By then Lee Bowyer had already gone with a hamstring injury and Matt Jackson made it two each when he departed with a knee injury and just before the break illness forced off Lee McCulloch.
A Bramble challenge on David Thompson earned Wigan a fourth minute free-kick and Bullard scored with an exquisite 23-yard free-kick.
Ameobi then missed with the goal at his mercy after 17 minutes heading wide Charles N'Zogbia's free-kick before it was all level after 26 minutes.
Michael Chopra - on for Ameobi - looked to be held by Reto Ziegler and linesman Mike Cairns signalled for a spot kick which saw Shearer stick away for goal number 204 for his hometown side.
With De Zeeuw and Jackson off injured, the Wigan central defence had to be repaired and it was caught all over the place after 33 minutes when Bramble was allowed a free header to power in Nobby Solano's right-wing corner.
The fit-again Keiron Dyer was revelling in his midfield role and set up a chance for Chopra after 36 minutes which was blocked on the line.
The next goal was always going to be crucial and it nearly came from an unlikely source when Robbie Elliott's cross dropped onto the bar.
John Filan then saved well from Solano but the ball still dropped behind him on to the line before spinning back into his arms.
Chopra, who was involved in Shearer's opener, then carved open his second with an inch-perfect through ball that saw Shearer race through to round Filan before firing into the net.
Chopra then created another chance for Shearer whose effort this time flashed wide of the far post.
Wigan by now were a spent force as they suffered their first ever league defeat against Newcastle.