The 28-year-old has been used in 27 of the Toffees' 31 top-flight games this term and also featured twice in the Europa League.
"My squad is almost complete, but 'Gana' had a muscle tear when he came over," he told reporters. "I had wanted him to be in my team, but I think he will be out for three weeks.
"I wanted him to come over with the rest of his national teammates, so we could assess his injury. He was able to do so."
As well as sitting out Everton's next couple of league games, Gueye will also miss Senegal's friendlies with Uzbekistan and Bosnia-Herzegovina.