West Ham came from behind to snatch a last-gasp victory thanks to skipper Nigel Reo-Coker's close-range tap-in.
Wigan had taken the lead just before the break with a stunning long-range drive from Lee McCullough.
But Paul Scharner's weak header back to Wigan keeper Mike Pollitt dropped short allowing Harewood to round the substitute keeper and tap in to level.
The game looked to be heading for a draw before Teddy Sheringham crossed for Reo-Coker who cooly slotted home.
The result means that Wigan have yet to take maximum points from a home Premiership encounter in 2006.
But the home side started the brighter and had the first opportunity when Jason Roberts teed up Gary Teale who drove his long-range shot straight at West Ham goalkeeper Shaka Hislop.
Former West Ham midfielder Jimmy Bullard then bent in a free-kick that forced Hislop into a low save in an opening first quarter of limited chances.
In a first period devoid of quality and inspiration, Wigan's strike duo of Roberts and Henri Camara looked the more likely to break the deadlock.
Roberts had a half chance after 36 minutes with a swivelling shot that flew over the bar while at the other end Dean Ashton played in Reo-Coker who saw his goalbound shot blocked by Leighton Baines.
Lee McCullough almost gave the below-average attendance something to cheer when he fizzed in a fierce left-foot shot that Hislop did well to palm over.
And it was the Scot who finally injected some quality into the match when his stunning long-range drive left Hislop rooted to the spot handing the home side the lead a minute before the interval.
Wigan were forced into replacing goalkeeper John Filan at half time because of an eye injury sustained in a collision with Harewood earlier in the half.
Pollitt came on for his first appearance since picking up a hamstring injury in the Carling Cup final.
Soon after the restart Camara's invention saw him break through the West Ham defence only for the Senegalese striker to steer his shot straight at Hislop.
The Hammers were quick to regroup and immediately responded with a fortunate goal from Harewood.
A long pass from Hislop caused confusion in the Wigan defence and Harewood's persistence and strength forced Scharner into a poor header back to Pollitt allowing the striker to round the substitute keeper and tap in.
Scharner almost redeemed himself after his dreadful error minutes later when his powerful header from a corner was cleared off the line by Scaloni.
McCullough almost bagged his and Wigan's second with a stinging volley that Hislop did well to repel and Camara almost won it for the home side in a goalmouth scramble that was hacked to safety with five minutes remaining.
As both teams went in search for the winner, the game opened up, and substitute David Thompson had a fine chance to win it for Wigan at the death, but his header from close range just drifted wide of the post.
And two minutes into stoppage time, substitute Sheringham squared for the West Ham captain to steal all three points.
"It is something that needs to be addressed for next season because it is going to be a lot tougher than this one - if that's possible.
"Other than the four we scored against Manchester City and the three against Charlton Athletic, we have found it a struggle to score goals at home."
"Now there's a chance of glory and we have to grasp that opportunity.
"The FA Cup is a chance to win a trophy. Sixth or seventh place in the Premiership doesn't really enthral me as much as winning silverware."
Wigan: Filan (Pollitt 45), Chimbonda, De Zeeuw, Scharner, Baines, Teale (Thompson 70), Bullard, Kavanagh (Ziegler 75), McCulloch, Roberts, Camara.
Subs Not Used: Jackson, Johansson.
Booked: Kavanagh, McCulloch, Thompson.
Goals: McCulloch 45.
West Ham: Hislop, Scaloni, Collins, Gabbidon, Konchesky, Benayoun (Newton 90), Reo-Coker, Mullins, Etherington (Zamora 71), Harewood, Ashton (Sheringham 81).
Subs Not Used: Walker, Clarke.
Goals: Harewood 52, Reo-Coker 90.
Att: 18,736
Ref: D Gallagher (Oxfordshire).