The Spaniard has argued all season the 21-year-old should not be considered for the tournament in the Czech Republic because of his progress with the senior side, and Southgate has agreed.
Martinez welcomed the move, insisting midfielder Barkley will benefit more from a well-earned rest ahead of next season.
“We work together with England and we are always there to help,” said Martinez, speaking at Everton’s annual awards night.
“I think Ross is a player who has already been in a tournament (the World Cup in Brazil) with the senior side and it is common sense when you are in the U21s and go into a big tournament it is to prepare you for the seniors.
“I think with Ross it makes sense he is allowed to concentrate on the senior squad.
“He hasn’t been involved in the (U21) qualifying rounds and I think it makes sense the team that qualified stayed for the tournament.
“He needs a good break. I think it has been an incredibly mature role the one he has developed this season without catching real highlights.
“He deserves a good break and we are very excited about the future of Ross.”
Everton do have John Stones and Luke Garbutt in the U21s squad but Martinez is pleased for the pair to have the chance to experience a major tournament.
“John and Luke can help England to be successful,” he said.
“In the case of John as we all know he has one of the brightest careers in English football, and I don’t say that lightly.
“He had an injury earlier in the season but he is now in a situation where he can be a leader.”
Stones won Everton’s young player of the year award while Brendan Galloway, who made his first-team debut against West Ham last weekend, was named U21 player of the year.
Toffees captain Phil Jagielka had a clean sweep winning player of the season, player’s player and goal of the season for his long-range strike in the Merseyside derby at Anfield.
“It is always nice to win personal things but as captain of this team I’d have like to have won with us pushing for European and Champions League places,” said the England centre-back.
“That would have made the award that more sweeter.
“We have quite a few young lads in the team so hopefully they will have learned just as much from this season as they did from last season.
“Considering the standards we set ourselves and we’ve had a bit of disastrous season, but we’ve actually picked up a decent amount of points and some good results along the way.
“It’s not been all doom and gloom; we expected to be higher up the table for the majority of the season but it never materialised.
“We are not that far away so we won’t beat ourselves up too much.”