The 30-year-old England international underwent surgery to correct the ongoing problem he aggravated on the training pitch on the eve of the Premier League season.
Toffees manager Roberto Martinez confirmed the news following Saturday's game against Watford: "Everything had been perfect in Leighton's programme and he worked extremely hard in pre-season.
"He looked refreshed, he looked strong and he look at a really, really good level.
"Then, in training, he blocks a ball and it hits him exactly in the same area where he had surgery [in May], with the unfortunate result that he's going to be out for a while.
"It's one of those tough moments that you have to take as a player but he knows we're going to help him immensely, everyone will support him and we have to make the most of his other role, which is to be part of the group and be a leader while he's getting back to full fitness."
Baines is set to be sidelined for 12 to 14 weeks.