Martinez described his side’s display as their worst of the season, but he was impressed by the impact that Stones made after coming on at half-time.
“I think he has come back with a real focus and a real intent of performing well and I think the second half performance, the back three had to do everything, defend, get on the ball and try to play forward and I thought it was an all-action performance," the Spanish boss said.
“He reacted well and anticipated things very well. He played really well, and he’s refreshed.”
Arsenal were already 2-0 up when Stones entered the action at half-time, after dominating for the opening 45 minutes.
Arsene Wenger’s side scored twice early on through Danny Welbeck and Alex Iwobi, and they were rarely threatened throughout the rest of the contest.
Everton’s performance was highly disappointing, but Stones did seem to steady things up at the back after being introduced.
The England international has dropped out of favour at Everton recently, but he could be set for a run of games over the coming weeks.
The Toffees’ next match comes against Manchester United after the international break.