The Everton manager chose to travel without the duo as his side won 2-0 against Hull City in their last game of the season.
Roy Hodgson is set to name his party at 2pm today ahead of the international tournament in Brazil, but Martinez is adamant it had no influence over his decision.
Instead, the Blues boss says he did it purely ‘in the interest of the health of the player’ and to see how others fared at the KC Stadium.
“There were three players that I had to protect,” said Martinez.
“Ross and John were two and Antolin Alcaraz was the third.
“Antolin after having a few niggles and injuries during the season, so we had to protect him, and I wanted to see other players that have been out injured.
“Before you send them away on holiday, you want to see where they are. They passed the test so they can have a bit of time off.
“(Barkley and Stones) will be busy (in the summer) because, as you know, it can always be the opportunity of representing the seniors side. If not, they’re going to be with the under 21s in the Toulon tournament.
“One way or another, they’re going to busy and that was one of the reasons that we had to look after them a little bit and make sure they didn’t go in to the summer with a risk of injury.
“Now they’re fine, they’ve been regenerating all week, and they’re ready for whatever comes their way.