The 36-year-old overhauled Irishman Dan Martin in the final 300 metres to add to his fifth win at Fleche Wallonne on Wednesday.
"This win is for Michele Scarponi. He was a good friend of mine," said an emotional Valverde.
Italian Scarponi died in a training accident after being struck by a van in central Italy on Saturday.
"It hurts to think he's gone, I'll miss him. I'll give all my prize money from this victory to his family. This win is also dedicated to him."
It has been a remarkable start to the season for Valverde, who turns 37 on Tuesday.
He has won four stage races – the tours of Catalonia, the Basque Country, Andalusia and his home region of Murcia – already this season, and two one-day classics.
