Wigan, marking the end of 23 years of ownership by the Whelan family, took an early lead when on-loan Reece James bent a superb free-kick past Bailey Peacock-Farrell from 25 yards.
But with Belgium boss Roberto Martinez watching on at his old club, Leeds got back on level terms within three minutes when Mateusz Klich crossed for Pablo Hernandez to slot home.
Hernandez turned provider as Leeds nudged ahead in the first minute of the second half, his cross badly fumbled by Walton for Kemar Roofe to score his sixth Championship goal of the season.
James and Callum McManaman sent efforts off target as Wigan sought an equaliser but Hernandez nearly added a late third, thudding a drive against the post with Walton beaten.
Paul Cook's side slipped to a fourth defeat in its past five league matches and remain in the bottom half, while Leeds move top on goal difference.