The England international was substituted five minutes into the second half and could now face six weeks on the sidelines with the injury.
Baines had played the entirety of Everton's Premier League season before being withdrawn, while also being an ever-present in the top flight during the last campaign.
Manager Roberto Martinez said: "It has been confirmed that Leighton has got a fracture in one of the bones in his right foot, which is the phalange.
"We need to treat that now and see how it develops. It could mean anything from missing six weeks to being back in 10 days because it depends how the fracture heals.
"It is in such a specific spot and we are going to see how it (the injury) reacts."
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