The England international goalkeeper landed awkwardly on his shoulder as he made contact with team-mate Ben Mee after claiming the ball in the air.
Heaton was substituted in the 31st minute of the clash against De Boer's Palace and was replaced by Nick Pope, who made his Premier League debut.
The substitute shot-stopper took to the Turf Moor pitch with his side 1-0 in front of struggling Palace on Sunday afternoon and managed to keep a clean sheet to secure the win for his side.
An early goal from Chris Wood after just three minutes, following a disastrous back-pass from Lee Chung-yong, was enough to ensure the three points went to Burnley.
Sean Dyche's side will hope Heaton's injury is not a serious one as they have some very tough fixtures coming up in the Premier League, with Liverpool, Everton and Manchester City all to play in their next five matches.
Heaton will also be hoping it is just a brief spell on the sidelines as he looks to claim the England No. 1 spot from Joe Hart, who has been unconvincing recently.