In the other repechaje matchup, Atlas faces Necaxa. Cruz Azul, Monterrey and Toluca move straight into the quarterfinals.
Santos Laguna, for which New Mexico product Castillo played nine games while missing part of the season with Mexico U-23 national team duty, finished two points behind Chivas in the overall standings.
San Luis was the surprise team of the Clausura 08 with a fourth-place finish in the overall standings, but didn't qualify automatically for the quarterfinals because it finished third to Chivas and Cruz Azul in Group 3.
Last weekend, Torres played the final 33 minutes in Pachuca's scoreless tie at Pumas. Castillo went the distance in Santos' 4-1 win over San Luis and Hernandez went 90 minutes in Jaguares' 2-2 tie with Chivas.
Hernandez, the former New England Revs midfielder, has started 11 games for Jaguares this season.
Padilla, who spends most his time with Chivas' reserve team, played two first-team games this season.
Californian Sammy Ochoa was a 63rd minute sub for Tecos in a scoreless tie with Veracruz. It was the 21-year-old's first first-team appearance since February of 2007.