The Latics had a stranglehold on the points from the half hour mark as they swapped places with Shrewsbury.
Wigan were ahead after 14 minutes with Will Grigg glancing in Lee Evans' near-post free-kick.
It stung Rotherham into action and they levelled just two minutes later with David Ball curling in a stunning effort from the edge of the box.
The visitors responded with several dangerous crosses pumped into the area before Alex Bruce put them back in front after 28 minutes with an inventive finish.
Rotherham had been under heavy pressure before Bruce, with his back to goal, flicked an effort beyond Marek Rodak.
Wigan made their position safer on the hour with Michael Jacobs firing in after Grigg had been superbly denied one-on-one with Rodak.
Ryan Colclough was Wigan's dangerman throughout the game and he almost scored a fortunate fourth when his cross was deflected goalwards and palmed out by Rodak on the line.