The Movistar rider joins Belgians Eddy Merckx and Marcel Kint as well as Italians Davide Rebellin and Moreno Argentin as triple Fleche champions.
“It was really a very hard day, with a lot of crashes and a lot of tension," Valverde was quoted as saying by Cyclingnews.
"I can’t remember such a tense day for a long time."
Valverde powered away from the thinned-out pack with about 200 metres left in the Mur de Huy, a 1.3-km ascent at an average gradient of 9.6 percent to beat France's Julian Alaphilippe (Etixx-Quick Step).
Swiss Michael Albasini was third for Orica Green-EDGE in a crash-marred race that saw 2013 Tour de France champion Chris Froome hit the tarmac 12 kilometres from the finish.
The Team Sky rider, one of the pre-race favourites for this year's Tour, went back on his bike with bruises on his left thigh and crossed the line 12 minutes and 19 seconds off the pace.
Former world champion Philippe Gilbert, the 2011 winner, abandoned the race after sustaining injuries in a crash 50 kilometres from the finish.
Tour de France champion Vincenzo Nibali of Italy jumped away from the pack in the penultimate climb, the Cote de Cherave, with about five kilometres to go but his effort was short lived as he was counter attacked by Belgium's Tim Wellens.
The Lotto-Soudal rider built a 15-second gap but he could not hold off the pack in the final climb, allowing Valverde to retain his title.
The Mur de Huy will serve as finish of the third stage of the Tour de France on July 6.
(Writing by Julien Pretot, editing by Pritha Sarkar; Editing by XXXX)
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