The England international was named in the starting eleven before Everton were forced to change their starting line up.
Experienced centre-back Phil Jagielka slotted in alongside Kurt Zouma.
Keane dropped out in the warm up after not feeling well enough to take part in the match.
James McCarthy comes onto the bench to replace Jagielka.
The former England international was given an early wake up call when he lost track of Alexandre Lacazette.
The Frenchman dragged his cross wide of the goal, he felt the force of Zouma’s challenge in the aftermath of the coming together.
Everton did receive some good news when it looked as if Lucas Digne was set to follow Keane out of the starting team.
The left-back was moving gingerly during the warm up.
But they would have been delighted to see the Frenchman lined up in the tunnel and ready for action.
He was also on the receiving end of a nasty challenge from compatriot Matteo Guendouzi.
It was Jagielka of all people who gave Everton the lead inside ten minutes, he wasn’t even supposed to be in the starting line up.
The goal was his first in the Premier League for two years.