Hernandez left the South Americans to join Manchester United before the World Cup and immediately impressed during pre-season.
The 22-year-old scored in the Community Shield win over Chelsea and made a late cameo in United's 3-0 victory over Newcastle in the Premier League on Monday.
But the Mexican's move to Old Trafford means he has missed out on the chance to scoop Latin American football's top club prize.
Chivas face Brazilian outfit Internacional in the second leg of the Copa Libertadores final on Thursday and the Mexican side have a mountain to climb after losing the first leg 2-1.
Vergara said: "It won't be easy, but the team are convinced they can turn it around."
Internacional midfielder Sandro signed for Tottenham earlier this year, but the Brazilians insisted the player remained until the end of their Libertadores campaign.
And Vergara now wishes he had negotiated a similar deal for Hernandez.
He added: "I am certain he would have made an important contribution against Internacional.'
"Maybe our mistake was not having kept Javier at Chivas until the final.