Uwe Rosler's men had lost their last three away games, all without scoring, but they left Hillsborough with the points thanks to two Nicky Maynard goals in the space of seven first-half minutes and Marc-Antoine Fortune's effort at the death.
Maynard's first effort ended Wigan's 322-minute wait for an away goal in the league and set up a first victory on their travels since January 1.
Wednesday will contest that the scoreline was not a true reflection of the game, though, as they dominated the majority of it, but Atdhe Nuhiu was twice wasteful and Stuart Gray saw his side's 11-game unbeaten streak ended.
Wigan did enough when it mattered and will feel that justice was served after their original visit to South Yorkshire was called off due to a waterlogged pitch before Christmas when in a commanding position.
The Latics were aggrieved at the abandonment as they were winning 1-0 and playing superbly when the surface became unplayable and they initially struggled to recreate the verve they managed on that wet December night.
In fairness, Wednesday are a different proposition to the one of a few weeks ago and they started brighter, though were restricted to half-chances.
Defender Miguel Llera spotted Ali Al Habsi off his line from a free-kick and fired in an effort from the halfway line that went just wide and then Benik Afobe also sent a low effort wide from an acute angle.
The hosts were presented with their best opportunity after 27 minutes.
Leon Barnett was caught in possession on the left by Nuhiu and he closed in on goal, but the lanky striker's weak effort was easy for Al Habsi to save.
And the Owls paid the ultimate price for that miss as Wigan stole the lead four minutes later, finally ending their barren run on the road.
Maynard received the ball on the edge of the area and drove a low shot across Chris Kirkland into the bottom corner, netting their first away league goal in over five hours.
They only had to wait another seven minutes for their next one as they put themselves firmly in the driving seat when Maynard struck again.
Waghorn whipped in a low corner to the near post which crept in, with Maynard credited as getting the final touch on the line.
Wednesday tried to regroup, but after 10 minutes of the second half Gray had seen enough and brought on Jeremy Helan and Michail Antonio on and it almost paid immediate dividends.
Helan had time and space on the left and drilled a fierce effort from 25 yards out that Al Habsi did brilliantly to claw over the bar.
The Owls were hampered by a serious looking injury to Jose Semedo, who left the pitch on a stretcher, but they laid siege in Wigan's goal in the final third.
Nuhiu headed wide a good chance and then Al Habsi did well to palm away a vicious Chris Maguire effort from distance.
Wigan ensured that eight minutes of added time would be served out with ease as Fortune put the game to bed when he had the easiest of tap ins after Kirkland had parried Maynard's low effort.