A statement from Wigan chief executive Jonathan Jackson read: "Whilst we appreciate that the vast majority of supporters who ran on to the pitch did so spontaneously to celebrate a famous victory, we were disappointed with the action of a minority of supporters who acted in an inappropriate manner. Player and staff safety is of paramount importance and we will conduct a full investigation.
"However, it is important to not let the actions of a few supporters detract from an incredible night at the DW Stadium. A special atmosphere was created by both sets of supporters and the match was yet another memorable day in the history of Wigan Athletic."
There were also tense scenes in the tunnel at half time as Guardiola and Wigan boss Paul Cook clashed over Fabian Delph's sending-off in the first half.