Jagielka appeared to jar his knee in a collision with Alex Oxlade-Chamberlain early in the second half and immediately crumpled to the ground in pain.
The 33-year-old hobbled to the sidelines and was replaced by Ramiro Funes Mori, but the severity of the injury is not yet clear.
Roberto Martinez conceded after the game that the injury was the biggest negative of the afternoon, but the length of any lay-off is not yet known.
Jagielka will no doubt go for a scan, but it already seems likely he will miss Tuesday's League Cup tie against Norwich, with Evertonians hoping it is not much more serious than that.
"Phil Jagielka doesn't complain often so for him to come off it must be an injury. It’s probably the biggest negative from today.
"It's too early to tell but it's his right knee and it could be one of a number of structures that are damaged.
"We’ll see what the next 48 hours bring."