The Manchester City winger failed to make the final 23 for the tournament in Brazil and will miss out on a second World Cup.
Navas had been struggling with injury during the weeks building up to the squad announcement, but had regained full fitness.
However, Del Bosque opted to drop him from the squad along with City team-mate Alvaro Negredo, a decision Navas feels will prove to be the correct one.
"It is a shame. I have worked hard to (to gain fitness) but it is the boss who makes the decisions and he always makes the right ones," he told AS.
"He has done what is best for the group. The truth is that I have recovered and was geared up but there also many of my team-mates who share the same dream.
"The main thing is to work with humility. It was a very exciting opportunity but we have all worked to be included and it is the coach who decides.
"I just want to wish my team-mates luck, it’s a great opportunity and I hope they can win the title again."
Spain will target a third consecutive international title in Brazil, after winning the 2010 World Cup and the European Championships in 2012.
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