Ex-Celtic boss Lennon has now led his Bolton side to four wins in six matches, form that has seen them climb out of the relegation zone and up to 18th.
They had to withstand a first-half barrage from the visitors, though, before taking control as all four goals came after the break.
Wigan burst out of the blocks and created several early chances, the best of which fell to Callum McManaman.
He was denied by the crossbar in the sixth minute with a strike from distance and hit the woodwork again on the stroke of half-time.
Bolton made Wigan pay for their missed chances five minutes into the second half, Max Clayton running down the left before slotting past goalkeeper Scott Carson.
Craig Davies doubled Bolton's advantage in the 55th minute, nodding in Liam Feeney's cross, and they made sure of their win just after the hour mark with Lee Chung-yong's penalty.
McManaman netted a deserved goal 11 minutes from time, finishing James McClean's run and cross with aplomb, but it mattered little for a Wigan side who drop to 21st - above the relegation zone on goal difference alone.
