The Brazilian was left with mixed emotions following the Barcelona keeper's knee injury, while Jordi Alba admitted the news will have a "significant" effect on the squad.
The Brazilian scored twice in a comfortable 3-0 victory at Camp Nou, but Spain international Valdes was stretchered off in the first half with what was later confirmed as a ruptured ligament in his right knee.
With Valdes set to miss the World Cup and unlikely to feature for Barca again as he prepares to leave in the summer, Neymar was left with mixed emotions after the win.
"I'm happy that we won. I'm very happy for the two goals and that we won the other day in the [Santiago] Bernabeu. On a personal level, I'm very calm and feel at ease," he told the club's official website.
"The victory is bittersweet because of Valdes' injury."
Defender Jordi Alba went on to admit that the whole squad has been hit hard by the 32-year-old's injury.
"It's a very serious injury on a personal level and also for the whole team. His absence will be significant," said the Spain fullback. "We've shared a lot of time together and it's always a shame when a teammate picks up an injury, even more so when it's Victor Valdes.
"The team needs to follow the path we've taken thus far. We've secured a string of good results, we're on form and we have to try to win the games we have left and hope that Real Madrid and Atletico [Madrid] lose points."
Sergi Roberto, meanwhile, was confident that Jose Pinto and Oier would be ready to step up to the plate as Barca prepares for a derby clash with Espanyol on Saturday.
"We're affected by his injury, but Pinto and Oier are great keepers. Now we have to fight until the end of the Liga. There aren't many games left and it will be exciting until the end," he said.
"The derby against Espanyol is always a good match to play in, it will be a final."