The former Arsenal man, who has been the subject of bids from Manchester United this summer, was brought off in the 82nd minute of Saturday's game and will now be assessed ahead of the Primera Division opener against Levante on August 18.
A statement on the club's verified Twitter feed read: "@cesc4official has sprained his left ankle. The player will undergo further tests to determine the severity of his injury."
Lionel Messi missed the win in Kuala Lumpur due to a thigh strain but his absence was thought to be merely a precaution.
Fabregas had scored the opener and set up further goals for Neymar and Gerard Pique before he was substituted as Barca cruised to victory in their final pre-season contest.