Jagielka started all of Everton's previous nine league games this season, with his late substitution in the most recent of those, a 2-1 loss at Burnley, the only time he had not completed the full duration.
He endured a torrid time in the match before that, giving away two penalties - both of which were saved by Maarten Stekelenburg - in a 1-1 draw at Manchester City, a game that came just over a week after he withdrew from the England squad with a thigh injury.
Koeman said of his decision on Sunday: "Not always, but sometimes with Jag it is a fitness question.
"I had already thoughts before the Burnley game. I like to protect Jag.
"November, December and January will be very tough for everybody, and sometimes you need to give players the opportunity to show.
"That was the reason finally that I changed and gave the opportunity to Funes Mori to start."