Coyle only took over at the DW Stadium in June following Roberto Martinez's departure to Everton.
The former Burnley and Bolton Wanderers boss exits with Wigan, who were relegated from the Premier League last season, 14th in the Championship.
Barnsley and Sheffield Wednesday are also seeking new managers after the respective sackings of David Flitcroft and Dave Jones over the weekend.
A statement on Wigan's official website confirmed the end of Coyle’s reign, adding: "Both (chairman) Dave Whelan and Owen Coyle have agreed that this is the right course of action in the best interests of both parties.
"The club wishes to place on record its thanks to Owen Coyle and to wish him the best in the future."
Coyle added: "It is with great sadness that we have made this decision and I would like to thank all of my football staff and the staff at the club, who have been very supportive of me in my time here.
"I am confident that with this set of players, the team can keep moving in the right direction."
A 3-1 defeat to Derby County on Sunday represented Coyle's final game in charge.
That loss was Wigan’s third in succession on home soil, with a 2-1 reverse against Zulte Waregem three days earlier damaging the club's hopes of reaching the UEFA Europa League knockout stages.
First team coach Graham Barrow and assistant manager Sandy Stewart will take charge for the league game at Leeds United on Wednesday.
