Baines converted a spotkick won by Kevin Mirallas on 87 minutes to earn a deserved point for the visitors.
Arouna Kone had put Wigan ahead on 10 minutes, taking advantage of wonderful work from Shaun Maloney to finish past Everton goalkeeper Tim Howard.
The Latics then took the lead on 23 minutes as the dangerous Franco di Santo finished a sweeping counterattack involving Kone and Gary Caldwell.
After the break, Everton dominated play and deserved their equaliser - a goal for Baines against his former club.
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