The Basques bossed the first half of their first-leg clash with the Partenopei, taking a deserved lead through Iker Muniain, only to see their hosts coming storming back after the restart, equalising through Gonzalo Higuain before repeatedly going close to securing a late winner.
Valverde conceded that his inexperienced players froze during that second-half onslaught, but he is expecting them to be much better prepared for Wednesday's return clash.
"At San Paolo we had some difficulties after their equaliser, but we also had very good phases when we could have taken a bigger advantage," the Athletic coach told reporters on Tuesday.
"Teams should be prepared to avoid those difficult moments, but if they can't avoid them, we should know how to react.
"It's also good to acknowledge that it's very difficult to dominate all the time; it's good to know what to do when your team have the initiative and when they lose it.
"But we think we are ready for this. We'll have to wait and see the result tomorrow but the players are really focused and motivated.
"They've been thinking about this match for months. The moment has come and the players should know how to manage that intensity.
"We're playing in San Mames – after completion this summer, the full new stadium will be inaugurated, so it's a special match. At similar games last season the team always responded well.
"Wednesday's match is a final because one of us will be eliminated. But today we're better than in the first leg against Napoli as we had a few players who were playing in the Champions League for the first time, so some will at least have that experience now."