Hernandez lasted 2 2/3 innings and took the loos after giving up nine runs on seven hits and four walks.
Hernandez, who was claimed off waivers from Minnesota on Wednesday, was 10-8 with the Twins before being designated for assignment on Aug. 1. He has a 5.48 ERA and 54 strikeouts in 139 2/3 innings this season.
The Rockies designated reliever Kip Wells, who has missed a large part of the season after having a blood clot removed from his right hand, for assignment.
Wells returned from the 60-day disabled list on July 21 and made his second start of the season that night against the Los Angeles Dodgers. He lasted 1/3 of an inning, giving up eight runs, seven earned, and seven hits in Colorado's 16-10 loss.
The Rockies also transferred first baseman Todd Helton to the 60-day disabled list, more than a month after the slugger was put on the 15-day disabled list.
The last time Helton played was July 2 against San Diego, two days before he was first put on the disabled list with a strained lower back.
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