The Portugal international said he felt a pain near his left ankle after 15 minutes of Sunday's 4-1 win at the Mestalla, but still managed to complete the game unaware of the extent of the injury.
"I was able to play on because it didn't hurt that much," Fernandes was quoted as saying on the website for sports daily As as he left Valencia's training ground on crutches on Monday.
The bone fracture was discovered after a medical examination on Monday morning. Valencia doctor Antonio Giner said the player suffered a blow to the leg during the game, and explained how Fernandes was able to continue without too many problems.
"He has a large muscle mass that held the bone in place, and in his case the shin is not heavily loaded," Giner said on the club website.
The 23-year-old will undergo surgery on Tuesday and is expected to be ready in time to start pre-season training with the rest of the squad for the 2009-10 campaign.
It is a blow for Valencia coach Unai Emery with his side chasing a place in next year's Champions League. They are fifth in the standings, two points off the top four and the qualification slots.
