Dembele was handed his first league start for the Catalan giants in Madrid, but the 20-year-old lasted just 25 minutes of the match after picking up a hamstring injury.
Barcelona are yet to confirm the length of the attacker's absence, and Valverde is remaining hopeful over the timeframe.
"Dembele? It looks like a muscle tear and it's a shame because he was getting into the team's dynamics and now it'll have to stop, hopefully not for long," Valverde told reporters.
Barcelona came from one goal behind to record a 2-1 win over Getafe, which stretched the team's 100% start to the new league season to four matches.