The former Arsenal and Manchester City defender replaced Liam Richardson in November after signing a three-and-a-half year deal.
But failing to win any of his matches during his two months in charge will see him leave the DW Stadium.
Kevin Betsy and Ashvir Johal will also leave the club.
In a statement, 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."
The Latics have collected just two points from seven league matches and are four points adrift from safety at the foot of the Championship.
They have a two-week break before facing Blackburn at Ewood Park on February 6th.