The Israeli, who has only just come back into the first-team picture, replaced Paul Bosvelt after 73 minutes but had to be replaced himself, by Antoine Sibierski, immediately after the tackle.
"I thought it was a very, very poor tackle from Bowyer," said the City manager.
City were already losing 3-0 at the time but Keegan is so miffed as Berkovic is likely to be out for City's testing trip to Poland.
He added: "It didn't cost us the game but we will have to assess the damage today, we have one or two niggly knocks and a lot of games coming up and we are going to need a full squad.
"Despite what people think we have not got a big squad at Manchester City.
"We have, I think, a fairly strong one in terms of experience, and I am happy with it but it is not as big as some clubs have got and we may get caught out with that. We will have to wait and see."