However, the Latics took just two points from his seven Championship matches at the helm and are bottom of the table, four points from safety.
They now have a two-week break before returning to action with a trip to Blackburn on Monday, 6 February.
"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," said Wigan chief executive Malachy Brannigan.
Wigan confirmed that two members of Toure's staff, Kevin Betsy and Ashvir Johal, have also left the club.
The remaining coaching staff will take interim charge of the the first team and Wigan say they are "working quickly to identify and appoint a new manager".
"I'd like to thank Kolo, along with Kevin and Ash, for their efforts during their time at the football club," added Brannigan.
"We know that this time of year is a key period for any football club, ourselves included.
"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."