Messi struck in the 36th minute before Paulinho sealed a tough 2-0 win for Barca, who were tested at San Mames on Saturday.
The Argentina international had released Jordi Alba down the left before getting on the end of a return pass to net his 12th LaLiga goal of the campaign.
Valverde was again full of praise for the 30-year-old, who has 16 goals in 15 appearances in all competitions this season.
“Messi could have scored another goal if the post hadn’t got in the way, but he’s incredible,” he said.
“He can make the difference at any moment. It was a spectacular goal.
“We’re so lucky that the best player in the world plays for us.”
Barca are four points clear atop LaLiga after winning nine of their opening 10 games, conceding just three goals.
Valverde was relieved to come away with three points against a club he played for and coached.
“It is important to win difficult games. Athletic caused us lots of difficulties,” he said.
“They raised the intensity and the ball spent more time closer to our goal than we got it to theirs. But we have shown why our defensive record is so good.”