However, the winning margin flattered Bolton although Nicolas Anelka also missed a penalty before grabbing the late fourth goal.
Had the Latics scored at the start of the second half when laying siege to the home goal, the final result might have been different.
However, Jussi Jaaskelainen pulled off two tremendous saves and fit-again Emile Heskey headed over the bar when it seemed easier to score.
Just as they had done against Manchester City last weekend, Wigan made a dreadful start as another defensive howler gifted Wanderers a third-minute advantage.
El Hadji Diouf's cross appeared to be harmless enough, but poor communication between Paul Scharner and Chris Kirkland led to the Austrian midfielder putting the ball into his own net.
However, the Latics were behind for only 11 minutes. Emmerson Boyce centred from the Wigan right and Abdoulaye Meite's half-hearted clearance landed at Denny Landzaat's feet. The Dutchman slotted the ball beyond Jaaskelainen from 18 yards for the equaliser.
Bolton should have restored their lead after 23 minutes. They had already had one penalty appeal for handball turned down when referee Martin Atkinson ruled that Andreas Granqvist had handled Danny Guthrie's shot.
Anelka took the spot-kick but, instead of celebrating his ninth goal of the season, he hung his head in shame after lifting the ball over the crossbar.
Bolton did restore their lead though eight minutes before half-time. Ricardo Gardner won a crucial tackle in the centre circle before Nicky Hunt picked out Anelka in the penalty area with a delightful pass.
The France international turned and fed Kevin Nolan who cleverly back-heeled the ball into the net from virtually on the goal-line for his first home goal since February 11.
It had been a rip-roaring first half and far more entertaining than most people had expected, and there was a cracking start to the second period as well.
Anelka badly miscued after being freed by Kevin Davies but the main pressure came at the opposite end.
Wigan forced a series of corners and Jaaskelainen did well to keep out efforts from Antonio Valencia and Marcus Bent while Heskey did not exactly show his England credentials with a weak header.
Bolton eventually lifted the siege and almost scored again themselves in the 56th minute.
Davies did well down the Bolton right and his cross was headed goalwards by Diouf only for Boyce to make a timely interception.
The Trotters did put the match out of Wigan's reach in the 70th minute. Diouf floated in a free-kick and Davies slid in at the far post for his first Premier League goal since the final day of last season.
And, in stoppage time, Davies turned provider with another cross. This time Nolan missed his flick but Anelka could not miss with his six-yard left-foot shot.