The 22-year-old has been a regular in the Brighton first team since arriving from Anfield at the beginning of the season, but was stretchered off late on in a goalless Championship draw with Huddersfield Town on Tuesday.
A subsequent X-ray taken at a local hospital showed a break just above the ankle.
"Our thoughts are with Joao - as this is a real blow to him after such a good season for the club - and we all wish him a speedy recovery and return to action," said Brighton manager Chris Hughton.
"He's been an important player for the club this season, both before and after I came to the club [in December], and I would like to thank him for his efforts during his time on loan here, and also Liverpool for allowing him to come."
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