Di Santo scored his first goal of the 2012–13 season in a 2–0 away win at newly promoted Southampton on 25 August, opening the scoring in the 51st minute with a finish high into the net from inside the area. He was an unused substitute as Wigan defeated Manchester City in the 2013 FA Cup Final, manager Roberto Martínez instead playing Arouna Koné and Callum McManaman in attack. On 30 June 2013, Di Santo was released by Wigan.