Rakitic will have to undergo surgery to correct the issue and is to have the procedure on Wednesday.
Barca have not said how long they expect him to be out for, with further communication expected after his operation.
"During the course of Tuesday’s match, Ivan Rakitic took a hit to the first finger of his left hand," a club statement said.
"This morning’s tests have confirmed that he has a fractured metatarsal bone.
"The Croatian will undergo surgery this evening, after which a statement will be issued to explain how the operation went and how long the player is expected to be out of action".