The Japan international was omitted for the matchday squad that lost to the Magpies at Old Trafford on Saturday and, speaking to reporters, Moyes confirmed that the playmaker had to have his stomach pumped to treat a "bad sickness".
"Shinji was very sick after the [Everton] game and he did a bit of training on Friday but he was low," said the Scot.
"All of the stats that we look at were low so we felt we had better not take a risk in case we got an injury by playing him.
"It was a bad sickness. He thinks he ate too much and he had to get his stomach pumped but I think he is okay."
United could slip to as many as 15 points behind Arsenal at the summit of the Premier League this afternoon if the Gunners beat Everton.