The former Ivory Coast and Arsenal defender was appointed as Liam Richardson's replacement on a three-and-a-half-year contract back in November with Wigan inside the bottom three of the Championship table.
Fast forward almost two months and Wigan are bottom of the table and four points from safety.
The Latics picked up just two points and no wins from Toure's seven Championship games in charge.
The Wigan chief executive, Malachy Brannigan, said: “Firstly, I’d like to thank Kolo, along with Kevin and Ash, for their efforts during their time at the football club. Unfortunately, the results on the field have not been as we would have liked and as tough a decision as this was, the board felt it necessary to give us the best possible chance of remaining a Championship club next season.
“We know that this time of year is a key period for any football club, ourselves included. Therefore, we will now work swiftly and effectively to ensure the right person is appointed as the next permanent manager of Wigan Athletic, with the immediate objective of remaining in the second tier for next season.”
This was Toure's first senior role in management but he had worked as an assistant at both Celtic and Leicester City under his former Liverpool boss Brendan Rodgers.
Toure was part of Arsenal's Invincibles side who won the Premier League title unbeaten in the 2003/2004 season.
He won another title with Man City in 2012 and also helped Ivory Coast win the Africa Cup of Nations in 2015.
