The 29-year-old moves to San Jose after spending the past three seasons with Anderlecht in Belgium, where he appeared in 22 games, including three Europa League matches.
"We've scouted Victor for several years," said Earthquakes general manager John Doyle. "We saw him play at the CONCACAF Gold Cup and were very impressed with his game. He's a great addition to the off season moves we've made so far and we look forward to having him in San Jose."
Bernardez has been capped 52 times by Honduras during his international career, including a start in the 2010 World Cup against Switzerland which ended in a 0-0 draw.
"Victor gives us another quality player in the center of our defense," said Earthquakes head coach Frank Yallop. "He's a big, tough and athletic defender who can also play well with his feet and distribute the ball. We're excited to have him on the squad next season."