Gareth Southgate's side went out in the group stage in the Czech Republic.
"We made the decision and I back it," Ashworth told the BBC's senior football reporter Ian Dennis.
"Youth teams are there to help develop players and give them experience to get into the seniors."
Liverpool forward Raheem Sterling, Everton midfielder Ross Barkley, Arsenal midfielders Alex Oxlade-Chamberlain and Jack Wilshere and Manchester United defender Phil Jones were among those eligible but not called up.
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Ashworth added: "Those players are established internationals. It's like being a first-team player and asking them to come back and play in the U21s. It's not necessarily the right thing to do.
"The players who hadn't competed in the two-year cycle and lead-up to the European Championship wouldn't be considered.
"The debate will be reopened now but we stand by the decision Gareth and I made. You never know when you drop players into a new group whether it'll be the right thing to do."
England, who had Premier League quality in Tottenham striker Harry Kane, Everton defender John Stones and new Liverpool forward Danny Ings, lost 1-0 to Portugal, beat Sweden by the same score but then lost 3-1 to Italy.
Ashworth had a key role in the FA introducing proposals - the 'England DNA programme' - in December aimed at improving England's prospects at major tournaments.
The plan is to co-ordinate the style, formation and tactics from the under-15 side upwards. And he believes improvements can be seen already.
"I don't want to hide behind the fact we're devastated to have been eliminated in the group stages," Ashworth said. "We're disappointed with the group that we hoped and thought might go a bit further. But there are some success stories.
"In order to win things at senior level, we need to develop players who can deal with the ball in all areas of the pitch. We have to prioritise that in the development teams.
"They're young players and they'll make mistakes - it will cost us games. We have to accept that. We can't after six months say that's wrong, let's just crash it down the other end as quickly as we can.
"We're starting to see a different kind of player come through the system now. Three years into EPPP [Elite Player Performance Plan] we're seeing players more capable with the ball. I believe it will stand us in good stead in years to come. Is it too soon now to see that? Yes, perhaps."
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FA chairman Greg Dyke set a target in 2013 for England to win the World Cup by 2022 and Ashworth is adamant that this remains a realistic goal.
"Yes I do believe that," he said. "I genuinely believe we have a lot of good young players in the system. We have the pathways getting better at clubs and international level.
"We've introduced an Under-15s, 18s and 20s in the past 12 months because we recognise we need to give our players more big-game experience.
"You've seen at this tournament we need players who are able to make decisions at the top level in the big games in order to win tournaments. But that takes time - it doesn't happen overnight.
"We're all doing the right things but we need to sit tight and be a little patient and let it run its course. I'm convinced it will."
Match of the Day pundit Gary Lineker criticised the "exasperatingly amateurish approach" not to select players such as Sterling, Wilshere and Barkley for the tournament.
"We never learn. What a wasted opportunity to gather invaluable international experience," the former England captain added on his Twitter page.
Former QPR midfielder Joey Barton, who won one cap for England, said the "culture is rotten" in English football, and criticised the power of the Premier League clubs.
"There doesn't seem to be the pride there once was at representing England at any level or a major tournament," he told BBC 5 live.
"We have a talent pool to match any nation. It's not the players or coaching staff. It's not one thing, it's an accumulation of many things.
"The culture in English football isn't changing. No St George's Park, no massive spend, no changing coach will change it. The culture is rotten from top to bottom. The England national team will underperform at every single tournament for this reason.
"The players think 'I'm too good for the under-21s, I've been in a senior squad - I don't want to go to a major tournament. I need to rest because I want to play in the Europa League or Champions League next year'.
"Or 'hang on it's better for my career not to go to this tournament'. Or their managers are saying it. That's the problem with the Premier League being stronger than the FA. It's impossible for England to build good teams.
"The FA should say to them if you don't make yourself eligible for the under-21s, then you won't be considered for the national team for however many years.
"I feel for Dan Ashworth, I feel sorry for Gareth Southgate, I feel sorry for Roy Hodgson. What they are trying to do is so difficult until they get the Premier League back in line."
Former England defender Danny Mills has been on an FA commission set up to assess potential improvements to English football.
He said it could take a decade for major improvements to come to fruition, and also suggested English players earning too much is to blame.
"We looked at this as a commission and decided things needed to change. Gareth has only been in the job two years. Things don't change overnight. Changing the way England play and players develop will take 10 years at least. That's what the Germans had to do before becoming very successful.
"Do they get too much too soon? It's very difficult for the coaching staff. Raheem Sterling doesn't want to play for Liverpool - he certainly would have caused more problems for the under-21s than he would have done them good.
"When me and Joey were coming through, playing for the under-21s and national team was massive kudos.
"That doesn't happen now, they're given so much so early in club football that England Under-21s has become secondary. There isn't the same desire to play for them. Spain and Germany still have the desire to play for their Under-21s - they get paid an awful lot less than our players.
"English players are paid too much and clubs put pressure on them not to go to the tournament - 'We want to save you for next season'. We have to change this culture.
"I can't believe players even consider not playing for the under-21s. Those players like Barkley or Sterling could have called Gareth up and said 'I want to be in your side'."
You can listen to BBC Radio 5 live's Dan Ashworth interview and the reaction to the England Under-21s' performance from Joey Barton and Danny Mills here.
England made the right decision to omit some of their Premier League players in the European Under-21 Championship, says Football Association director of elite development Dan Ashworth.