After a frantic first half in which Wigan belied their lowly status in the standings by carrying the game to the hosts, Chelsea went ahead on 62 minutes when Branislav Ivanovic tucked the ball away from five yards out despite being clearly offside from Raul Meireles's delivery.
Wigan surrounded referee Mike Jones but he refused to overrule his linesman as Chelsea raced back to their own half clearly delighted to be ahead. It was a poor decision with visiting manager Roberto Martinez continuing to berate the fourth official from his technical area.
Justice seemed to be done when visiting substitute Mohamed Diame clobbered the ball beyond home goalkeeper Petr Cech from outside of the box with eight minutes left.
Chelsea won it two minutes into four added on though when Fernando Torres clipped a post with a thumping volley from Didier Drogba's chip with Mata on hand to nudge the ball over the line.
It came only seconds after Wigan captain Gary Caldwell was denied a certain goal-scoring opportunity by a fine David Luiz tackle.
The result leaves Wigan second from bottom of the table with Chelsea only three points adrift of third-placed London rivals Tottenham, who were held to a 0-0 draw by Sunderland earlier in the day.
Chelsea are already in the last four of this season's Champions League, but need to finish in the top four to be certain of a place in next season's tournament with only three points now separating Arsenal, Spurs and Newcastle in the race for third and fourth spot in the table.
Certainly, with veteran campaigners John Terry, Frank Lampard and Ashley Cole sitting out the action, Chelsea struggled to bring their European form to the afternoon.
Wigan goalkeeper Ali Al Habsi was in splendid form for the visiting side as he swiped Gary Cahill's howitzer over his bar on 18 minutes before doing likewise to halt a Mata shot 18 minutes later. To complete an outstanding first half, he nudged a Drogba header over his bar in stoppage time in the first period.
Al Habsi saved from Drogba on 52 minutes before Chelsea finally found their contentious opening goal courtesy of Ivanovic, who cleared off his line a minute later from Franco Di Santo's effort.
There were chances at both ends in the closing minutes with Salomon Kalou sticking a shot into the side of a net from Torres's cross with Victor Moses almost setting up Connor Sammon before Mata had the final say.