Tour de France winner Wiggins began the day with a 28-second lead overall but pushed it to 30 after finishing fifth with two stages left.
Chaves set the pace by finishing in four hours, nine minutes and 13 seconds ahead of Spaniard David De La Cruz Melgarejo and third-placed American Tom Danielson.
The race continues on Saturday with a 143-kilometer stage from Santa Clarita to Pasadena.
“The boys really did a fantastic job and they really put me in a good position near the finish,” said Wiggins.
“I was really just monitoring Team Garmin-Sharp and Rohan Dennis. It wasn’t until the final 300 metres when I noticed there were only four us left in the chase group.”
This race concludes on Sunday but the profile of the two remaining stages means Wiggins and his Team Sky team-mates should be able to defend their yellow jersey position.
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