Latics confirmed Stewart, who has been Coyle's right-hand man at Burnley, Bolton and his most recent employers, had left the DW Stadium following the 2-0 defeat to the Whites.
Stewart had aided caretaker boss Graham Barrow in selecting a team for the trip to Elland Road which came just three days after Coyle had seen his resignation offer accepted by Wigan chairman Dave Whelan, who claimed the regime did not get on with either him, the fans or the players.
Given Stewart's proximity to Coyle, the news comes as no surprise with Whelan looking to swiftly move on from the team he installed just six months ago.
A short statement on Latics' website said: "Wigan Athletic can confirm that assistant manager Sandy Stewart has left the club following the departure of Owen Coyle.
"Wigan Athletic would like to place on record its thanks to Sandy and wish him good luck in his future career."