The 41-year-old was appointed to his first managerial post on a three-and-a-half-year contract on Nov. 29, replacing Leam Richardson, but has failed to improve the Latics' fortunes at the bottom of the Championship.
Wigan were 22nd when Toure took the reins, but are now at the foot of the 24-team table, on 25 points, four from safety and without a win since Nov. 12, before the pause in competition for the 2022 World Cup.
His record after nine matches reads won zero, drawn three, lost six, with the 2013 FA Cup winners falling to home defeats in their last two matches.
"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," Wigan chief executive Malachy Brannigan said in a club statement.
"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."
Toure, who previously assisted Brendan Rodgers at Celtic and Leicester City, departs from the DW Stadium alongside coaches Kevin Betsy and Ashvir Johal, both of whom have also been relieved of their duties.
The former centre-back made 353 appearances in the Premier League with Arsenal, Manchester City and Liverpool between 2002 and 2016, becoming one of only eight players to win the title with two separate clubs.
With the Cote d'Ivoire, he amassed 120 caps and was an Africa Cup of Nations winner in 2015, while also representing the Elephants at three World Cups.
"We are delighted that Kolo has become the new manager of Wigan Athletic Football Club, and the board are pleased that he is the man to take us forward," Brannigan said when Toure was signed less than two months ago. "We received a high calibre of applicants for the manager's job in recent weeks, in a very thorough recruitment process as we looked to appoint the right person for the role.
"From the earliest of conversations we had with Kolo, it was evident to us that he had instantly bought into the values of the club -- with his enthusiasm, knowledge and immense desire to work and be part of Wigan Athletic shining throughout the process."
Wigan have confirmed that the coaches remaining at the club will assume first team matters, with the second-tier strugglers not in action again until they travel to promotion hopefuls Blackburn Rovers on Feb. 6.