The striker was named in the preliminary squad for next month's tournament by Bafana Bafana coach Hugo Broos on Thursday despite not playing for Premier League club Burnley since October.
"Unfortunately at the moment he's not in a position where he can go to the national team, he just can't," Kompany said Thursday.
"His love for his country has no limits and his desire to do well has no limits but that would be going against the advice of every expert that has been assisting him in recent months."
Former Manchester City star Kompany added: "I'm a coach from African origin so for me the AFCON is very important and I feel very proud of any player representing us there because I think that tournament deserves the same importance as the Euros but, for his condition specifically, the human being, he's not at a stage yet where he can do any of that.
"Hopefully in the future he'll be able to do much more for everybody on the big stage but step by step."
Foster had scored three goals in seven league games for the Clarets before the northwest club announcing last month the 23-year-old was receiving specialist care.
No timescale has been put on his recovery but Kompany revealed Foster, who joined Burnley from Belgian side Westerlo in January, had returned to doing some work with the club.
"Lyle's making progress," said Kompany. "He's still receiving treatment but we've been fortunate that we've been able to work on the fitness side with him.
"His progress is what you would want it to be in terms of his mental health but physically, he's in a good place as well."
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