Shoya Nakajima gave the Blue Samurai a 15th minute lead in Belo Horizonte while substitute Daizen Maeda had a late chance to win it when put through one-on-one with goalkeeper Alexander Dominguez.
Angel Mena's equalizer on 35 minutes and teenage sensation Takefusa Kubo's potential injury-time winner being ruled out by VAR meant Japan came up short.
"They're learning to compete with top level opponents," said Moriyasu, who brought a mostly under-23 team to Brazil as several clubs refused to release regular first choice players.
"Our players need to learn as much as they can, with great humility, respecting their opponents and understanding that they can develop our football."
This squad will at least form the basis of the under-23 team that competes in next year's Tokyo Olympics.
But it was an inglorious exit for Asia's two guest participants in South America's flagship tournament.
Asian champions Qatar finished bottom of Group B with one point from three games, while the team they beat in February's continental final in the United Arab Emirates, again failed to win a match in their second Copa America participation.
However, they did improve drastically on their opening match -- a 4-0 thrashing by Chile -- in drawing their next two games against Uruguay (2-2) and Ecuador.
"It's a shame that we couldn't progress to the next stage, we need to improve," said Moriyasu.
"Football is improving in Japan and in Asia in a general manner. We've managed to play good matches against strong teams from all over the world."
Ecuador's goalscorer Mena said he felt proud of his team but bitter at missing out on the next round.
"What I take away is the team's attitude after the loss in the first game," he said, referring to a 4-0 humbling by Uruguay.
"A lot changed for the second match and the team played the football it is capable of. We had chances but did not convert them today.
"More importantly, the attitude and pride we displayed were paramount."
And the 31-year-old said his goal was scant consolation.
"We are eliminated and sad. It's great to score goals, but it didn't help much. We leave with a sour taste."
Defender Arturo Mina felt Ecuador had deserved more.
"Japan sat back in defense, we controlled the game. I think they managed two or three chances, but we were superior," he said.