Wallays edged Sven Erik Bystrom to snatch a first grand tour win after holding off a late attack from world champion Peter Sagan in a packed finale at the end of the mostly flat 186.1 km stage from Ejea de los Caballeros to Lleida.
Lotto Soudal rider Wallays broke clear only three kilometres into the stage alongside Norwegian Bystrom of UAE Team Emirates and Dutchman Jetse Bol of Burgos-BH.
The leaders stayed at the front for the bulk of the day, enjoying a gap of two minutes thirty seconds at one point, which was cut down to 52 seconds in the final 10 kilometres and then to nothing as the stage concluded.
Bol faded in the final few kilometres and Sagan took up the chase but was not quite quick enough and could only finish third as the peloton crossed the finish line immediately after.
Valverde finished 16th, three places ahead of Yates but gained no time on the Briton.
Yates holds a narrow 25-second lead over the 2009 winner heading into the two mountain stages in the Pyrenees on Friday and Saturday which will almost certainly decide the race winner before Sunday's procession through Madrid.
Spaniard Enric Mas is third, one minute 22 seconds behind Yates, while Miguel Angel Lopez of Colombia and Dutchman Steven Kruijswijk, fourth and fifth respectively, have an outside chance of catching Yates.
Friday's stage is a 154.4km ride from Lleida to Naturlandia in Andorra with a summit finish while Saturday is a short yet unforgiving 97.3 km charge through Andorra which will involve 4000 metres of climbing.
(Reporting by Richard Martin; Editing by Toby Davis)
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