Ahead of the La Liga clash at Mestalla – which Valencia won 3-1 – the home fans hurled items at Atletico's bus.
And the club announced they would be working with the authorities to punish those guilty.
A brief statement on the club's official website read: "Valencia CF deeply regrets [the] throwing [of objects at] the bus of Atletico Madrid on arrival at Mestalla.
"The club will [pursue] all measures at its disposal [and will be] working with law enforcement to track down the perpetrators of the incident.
"And if [perpetrators are] identified, [they] can not access Mestalla in the future."
Valencia scored all three of their goals in the first 13 minutes against the Spanish champions as they extended their unbeaten record this season.
Nuno Espirito Santo's side sit second in La Liga, two points behind Barcelona.
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