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.