A 3-0 loss to Switzerland in Manaus ended Honduras' campaign as they finished bottom of Group E without a point.
Speaking after the loss, Suarez said the time had come for a change at the helm and the 54-year-old believes Honduras have a bright future.
"I made the decision to step down five minutes ago. It's time for a change," the former Ecuador coach said.
"The new coach has a good squad at his disposal, we've got good young players and we're on the right track. I'll take positive memories from this experience and I'll always be a Honduras fan."
Xherdan Shaqiri starred for Switzerland with a hat-trick, including scoring twice in the opening 31 minutes at the Arena da Amazonia.
Suarez said a sixth-minute goal was a huge blow to his team, who still had a chance of progressing heading into the game.
"Unfortunately we didn't get the result we were hoping for. Their early goal gave them an advantage and made every counter-attack a threat," he said.
"Our second half was good and we had several chances but we just couldn't score. The whole country is disappointed and I'm sad because we didn't manage to reach the next round. That was our dream."
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