The 28-year-old winger has suffered a hamstring injury in the build-up to the clash and will be absent for the trip to Spain, as well as Swansea's Premier League encounter against Crystal Palace on Sunday.
Hernandez signed for Swansea from Valencia in August 2012 for a then-club record £5.55million after spending eight years at his hometown club over two spells.
However, he will not shake off the problem in time to play at the Mestalla on Thursday, with boss Michael Laudrup forced to alter his plans.
The Dane is, however, boosted by the news that striker Wilfried Bony will be available after overcoming the rib injury he sustained in Monday's 2-2 draw with Liverpool.
The match will represent the first time that the two sides have met in competitive action, and it is Swansea's first official game against any Spanish opponent.
The Welsh side qualified courtesy of their League Cup win in February, while Valencia made the competition thanks to a fifth-place finish in last season's La Liga.
Valencia manager Miroslav Djukic has no new injury worries going into the game, although his side have endured a difficult start to their domestic campaign, losing three of their first four matches to leave them 16th in the table.
Sunday saw them go down 3-1 away at Real Betis, and prior to Thursday's game midfielder Andres Guardado has called on his side to pull together and secure a result.
"We need to get our act together and come out with attitude," he said.
"The most important thing right now is to win the next match against Swansea."
