Portugal international Ricardo Quaresma scored 15 minutes from time as Porto emerged 2-1 winners in UEFA Champions League action at the Estadio Do Dragao.
Quaresma's match-winner came 17 minutes after Bilbao striker Guillermo Fernandez cancelled out Hector Herrera's 45th-minute opener.
The defeat - Bilbao's second in three matches - left the La Liga club languishing at the foot of the Group H table.
Valverde, however, has not given up hope of reaching the knockout rounds, despite Bilbao's nine-game winless streak in all competitions.
"Porto ended the first half strong and scored at a difficult time," Valverde said afterwards.
"We were better in the second, got level and were looking for the winner, but then they scored the second.
"We lost the match by the same score as last time [against BATE] but it leaves a better taste.
"But we have three games left and we have to make the most of our options."
