The ex-Cote d'Ivoire international departs Leicester City, where he was a first team coach under Brendan Rodgers, to take charge at the struggling Championship outfit.
Wigan, which is currently 22nd and embroiled in a relegation battle, dismissed Leam Richardson after six losses in seven games earlier this month, just weeks after he signed a new contract.
"We are delighted that Kolo has become the new manager of Wigan Athletic," chief executive Malachy Brannigan issued in a statement.
"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. We look forward to working closely with Kolo and his team."
Toure, a two-time Premier League winner during his playing days with Arsenal and City, will take charge of his first match on December 10 against Millwall.