Wigan initially surrendered a two-goal first-half advantage at the DW Stadium on Sunday, but secured all three points thanks to Callum McManaman's winner.
Ben Watson's 11th-minute penalty put Wigan ahead after Matt Mills handled in the area.
That advantage was doubled in spectacular fashion on 24 minutes by Nick Powell, who found the net with an acrobatic overhead kick.
Mills almost responded with a similar effort of his own on the stroke of half-time, and Bolton reduced their arrears early in the second period when Wigan failed to clear a free-kick, allowing Neil Danns to head home.
Danns saw another header rebound off the crossbar before Bolton levelled in the 64th minute.
Emmerson Boyce was adjudged to have fouled Lee Chung-Yong in the area and Andre Moritz levelled proceedings from the penalty spot.
However, the sides were level for just four minutes as McManaman kept his composure to sweep home a left-footed finish from Boyce's flick.
The enthralling contest almost had one last twist as Joe Mason narrowly diverted wide from a Moritz cross.
Yet Wigan held on for the three points, ending their four-match losing streak in the league and climbing to 14th in the table, two places above Bolton.
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