Winger Jermaine Pennant and striker Kenwyne Jones both came down with the bug at the start of the week. They have suffered high temperatures and flu-like symptoms.
Both players started in yesterday's Carling Cup defeat at West Ham, but were substituted during the second half.
Pulis said: "The two of them weren't feeling that brilliant after the Manchester United game, so we were a little bit careful with them.
"Kenwyne actually felt worse when he was up in London after he woke up from a sleep on Wednesday afternoon, but we persuaded him to give us an hour.
"He looked very good when he played.
"We didn't get back in until half past three this morning, so we've given them the day off."
Pulis is confident both players will be well enough to start against Everton on Saturday, but was set to assess them this evening.
He said: "They'll report back tonight and we'll look and see who's ready to go and who's not, because it'll be a tough game."
Despite some of his squad playing 120 minutes in the game at Upton Park, Pulis has no qualms about throwing them in at Goodison on Saturday.
"We'll make some changes, but the players work very, very hard on their fitness," he said.
"They get paid damn good money, so to ask them to play three lots of 90 minutes, or whatever it is, over a week, I don't think is too much.
"It's a mental thing as well as a physical one, and we'll try to get that right as well."
There was positive news on the contract front from Stoke today, as Danny Higginbotham signed a one-year extension.
The 31-year-old former Manchester United and Sunderland defender is now tied to the Potters until 2013.
Higginbotham has helped Stoke establish themselves in the Barclays Premier League since joining them two years ago following their promotion.
However, he has fallen down the pecking order this season, having not started in the league since the opening day.
Pulis said: "He may not be in the side on a regular basis at the moment, but he still has a crucial role to play, as do a number of other players in a similar situation.
"The fabric of a football club is made up of the whole cloth, not bits and pieces, so we are delighted Danny will remain a part of that."