Wanderers manager Gary Megson had rested nine players in midweek for this crunch clash at the JJB Stadium, but it made little difference.
His side played without fluency and rhythm while their passing was erratic and poor in a disappointing first half.
Despite Bolton having the numerical advantage thanks to Koumas' early sending-off it was Wigan who had the best of the opening 45 minutes.
Koumas was red carded for a reckless tackle on Cahill, although replays suggested the Welshman was unlucky to be sent-off.
It mattered little to Wigan who started brightly and came close through Heskey and Marlon King early on.
But despite the early pressure it took 34 minutes before the deadlock was broken.
It came through Heskey who superbly volleyed Melchiot's long throw past Ali Al Habsi from six yards out for 1-0.
Only seconds earlier Wigan had thought they opened the scoring when Paul Scharner saw his header cleared off the line by Ivan Campo.
Scharner was certain the ball had crossed the line and television replays suggested he may have had a case but it mattered little as Heskey hit the back of the net seconds later.
Jason Koumas was sent off in the fourth minute
The goal galvanised Bolton who pushed for an equaliser and Nolan was convinced his shot had been blocked by the hand of Emmerson Boyce as he struck goalwards.
Minutes later El-Hadji Diouf had the ball in the net but it was ruled out for an earlier foul by Nolan.
With half-time approaching tempers became frayed as Michael Brown and Campo kicked out at each other, but no action was taken.
Players from both sides carried the arguments into the tunnel with Brown and Campo having to be separated as they left the field.
To their credit Bolton looked a different side in the second period as they went in search of a vital point.
Matt Taylor, Nolan and Kevin Davies both went close in quick succession with Kirkland proving an unbeatable force in the Wigan goal.
Their best chance came with 25 minutes remaining when Davies appeared to have his goalbound header cleared off the line by the arm of Brown.
But despite furious protests from Bolton captain Nolan, no penalty was awarded as Wigan breathed a huge sigh of relief.
Bolton dominated possession in the final 20 minutes and Nolan had his header cleared off the line by Edman in the last minute but Wigan held on to secure a significant three points.
Wigan manager Steve Bruce
"It was a huge win for us and credit to the players for the way they battled with 10 men for nearly 90 minutes.
"There were some fantastic performances out there and in particular Emile Heskey's goal could prove to be vital for us.
"I've looked at the challenge and I don't think it is a red card. He's tried to win the ball, it's one footed and I think that because of the climate we are in, it is leaving the referees in a difficult position.
"I think if it hadn't been for the Eduardo tackle a couple of weeks ago then that would have been a yellow card."
Bolton manager Gary Megson
"There were a lot of harsh words said at half-time because that performance was not acceptable.
"We've rested players midweek for this game and clearly it hasn't worked because we didn't turn up or start well.
"We looked lethargic and leggy and weren't good enough and we are right in the cart.
"I've seen a replay of the Michael Brown incident and it did look like a handball but I think when you are down the bottom you tend to focus on these decisions a bit more."
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