Pienaar had to be carried off in the 60th minute after initially trying to play on, drawing boos from the home fan.
The full seriousness of Pienaar's injury was not immediately clear, but Moyes was still incensed that Portsmouth captain Aaron Mokoena escaped punishment for his challenge on the diminutive midfielder.
Moyes told evertonTV: "It's another late challenge. It's one of these late challenges which I'm sure will be picked up by the referee. We lost a player (Phil Neville) the other week against Fulham and now we may have lost another one. Before you know it they're going to be taking all of our players out if the incidents are not picked up on."