The Argentina star was surprisingly dropped to the substitutes' bench for the 0-0 Champions League draw in Turin on Tuesday, with Barca director of institutional relations, Guillermo Amor, describing it as "a technical decision" and not one made due to injury.
Valverde has now explained he believed Messi would be more useful as a second-half substitute as he expected Juve to be more open.
However, he would not confirm whether it was something he had agreed with Messi in the build-up to the match, with reports in Spain suggesting it had been decided some days ago.
"He has built up a lot of games and we thought this time he could come on for the second half," said Valverde, as quoted by AS.
"We thought the game was going to be tight at the beginning and then it could be opened up later in the second half. That's what happened."
When asked if he had agreed it with Messi this week, he replied: "These are internal decisions of the coach."
0-0 - Barcelona have recorded goalless draws in back-to-back games in Champions League for the first time ever. Strange. pic.twitter.com/vcQP2cMI33— OptaJose (@OptaJose) November 22, 2017
Barca, who secured a place in the last 16 and top spot in Group D with the draw, controlled much of the match without creating too many opportunities against a reasonably defensive Juve side.
Marc-Andre ter Stegen was forced to make a fine save from Paulo Dybala in second-half injury time, though, and Valverde was pleased to see his goalkeeper stay alert for 90 otherwise quiet minutes.
"We came with the intention of winning and we played with personality," he said. "They're a team who press a lot. We dominated for long spells, except in the final few minutes, in which they had the play and had the chance with Dybala.
"Our intention is for Ter Stegen not to have much work and he hasn't, because we've dominated a lot of games, but they had that chance, which was at the end of the game."