The five-time Ballon d'Or winner has struggled with injuries and after returning as a second half substitute in the win over Deportivo La Coruna last weekend, Messi scored a hat-trick in Wednesday's victory against Pep Guardiola's Manchester City.
"Nobody doubted Messi," proclaimed the Asturian coach.
"Whoever doubted him is a bit naïve."
Much of the pre-match talk had been dominated by Pep Guardiola's return to the Camp Nou and although Luis Enrique came out on top, he admitted that there is still a way to go in terms of qualification.
"This isn't a signal of intent, it just three more points and I'm certain that they will pay us back in Manchester," he said.
"Many things happened that don't usually occur: injuries, red cards, two teams that play the same way, and all of that causes errors.
"It is a comprehensive result which makes us stronger," Luis Enrique explained.