Baines was substituted shortly after half-time at Goodison Park following a tackle involving Liverpool's Jordan Henderson - the first time the England defender had failed to complete a Premier League match since 2008.
The left-back underwent an X-ray after the game and now faces up to six weeks out.
Speaking on Tuesday morning, Everton 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."
Martinez also revealed Baines was keen to play on in the Merseyside derby, despite picking up the injury.
"Once more it shows you what an incredible character we have as he never wanted to stay in the dressing room, he wanted to help the team but in the end he had to come off," he said.
"It is a real disappointment to lose Leighton for any space of days, never mind weeks."
Gareth Barry filled in for Baines at left-back, a role he performed early in his career, but he is unlikely to stay there as a short-term replacement.
"Obviously Gareth slotted in during the game and when you have got a player with that experience, he can play anywhere. I thought he did really well," said Martinez.
"We have got other players at the football club who can play in that position, from Bryan Oviedo to Tony Hibbert and Sylvain Distin to John Stones. We have got many options.
"It's going to be a matter of seeing how the players react in training and, first of all, seeing if Leighton is going to be okay."